<?xml version="1.0" encoding="ISO-8859-1"?><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<front>
<journal-meta>
<journal-id>1405-888X</journal-id>
<journal-title><![CDATA[TIP. Revista especializada en ciencias químico-biológicas]]></journal-title>
<abbrev-journal-title><![CDATA[TIP]]></abbrev-journal-title>
<issn>1405-888X</issn>
<publisher>
<publisher-name><![CDATA[Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Zaragoza]]></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id>S1405-888X2018000321108</article-id>
<article-id pub-id-type="doi">10.22201/fesz.23958723e.2018.0.143</article-id>
<title-group>
<article-title xml:lang="en"><![CDATA[Molecular docking: current advances and challenges]]></article-title>
<article-title xml:lang="es"><![CDATA[Acoplamiento Molecular: Avances Recientes y Retos]]></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Prieto-Martínez]]></surname>
<given-names><![CDATA[Fernando D.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Arciniega]]></surname>
<given-names><![CDATA[Marcelino]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[José L.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
</contrib-group>
<aff id="Af1">
<institution><![CDATA[,Universidad Nacional Autónoma de México Departamento de Farmacia Facultad de Química]]></institution>
<addr-line><![CDATA[Delegación Coyoacán Ciudad de México]]></addr-line>
<country>Mexico</country>
</aff>
<aff id="Af2">
<institution><![CDATA[,Universidad Nacional Autónoma de México, Instituto de Fisiología Celular Departamentonde Bioquímica y Biología Estructural]]></institution>
<addr-line><![CDATA[ ]]></addr-line>
<country>Mexico</country>
</aff>
<pub-date pub-type="pub">
<day>00</day>
<month>00</month>
<year>2018</year>
</pub-date>
<pub-date pub-type="epub">
<day>00</day>
<month>00</month>
<year>2018</year>
</pub-date>
<volume>21</volume>
<copyright-statement/>
<copyright-year/>
<self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_arttext&amp;pid=S1405-888X2018000321108&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_abstract&amp;pid=S1405-888X2018000321108&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_pdf&amp;pid=S1405-888X2018000321108&amp;lng=en&amp;nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="en"><p><![CDATA[Abstract Automated molecular docking aims at predicting the possible interactions between two molecules. This method has proven useful in medicinal chemistry and drug discovery providing atomistic insights into molecular recognition. Over the last 20 years methods for molecular docking have been improved, yielding accurate results on pose prediction. Nonetheless, several aspects of molecular docking need revision due to changes in the paradigm of drug discovery. In the present article, we review the principles, techniques, and algorithms for docking with emphasis on protein-ligand docking for drug discovery. We also discuss current approaches to address major challenges of docking.]]></p></abstract>
<abstract abstract-type="short" xml:lang="es"><p><![CDATA[Resumen El acoplamiento molecular automatizado tiene como objetivo proponer un modelo de unión entre dos moléculas. Este método ha sido útil en química farmacéutica y en el descubrimiento de nuevos fármacos por medio del entendimiento de las fuerzas de interacción involucradas en el reconocimiento molecular. Durante los últimos 20 años se ha modificado extensamente la técnica de acoplamiento molecular dando resultados precisos en la predicción de los modos de unión. Sin embargo, hay algunas áreas que requieren ser mejoradas substancialmente. En este trabajo se revisan principios, técnicas y algoritmos usados en los programas computacionales del acoplamiento molecular con enfoque en la interacción proteína-ligando aplicado al descubrimiento de nuevos fármacos. También se discuten las estrategias dirigidas a solucionar los principales retos de esta técnica computacional.]]></p></abstract>
<kwd-group>
<kwd lng="en"><![CDATA[Chemoinformatics]]></kwd>
<kwd lng="en"><![CDATA[computer-aided drug design]]></kwd>
<kwd lng="en"><![CDATA[drug discovery]]></kwd>
<kwd lng="en"><![CDATA[structure-activity relationships]]></kwd>
<kwd lng="es"><![CDATA[Descubrimiento de nuevos fármacos]]></kwd>
<kwd lng="es"><![CDATA[diseño de fármacos asistido por computadora]]></kwd>
<kwd lng="es"><![CDATA[quimioinformática]]></kwd>
<kwd lng="es"><![CDATA[relaciones estructura-actividad]]></kwd>
</kwd-group>
</article-meta>
</front><back>
<ref-list>
<ref id="B1">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Adeniyi]]></surname>
<given-names><![CDATA[A. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Soliman]]></surname>
<given-names><![CDATA[M. E. S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Implementing QM in docking calculations: is it a waste of computational time?]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2017</year>
<volume>22</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1216-23</page-range></nlm-citation>
</ref>
<ref id="B2">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Agarwal]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Mehrotra]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[An overview of Molecular Docking]]></article-title>
<source><![CDATA[JSM Chemistry]]></source>
<year>2016</year>
<volume>4</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>1024</page-range></nlm-citation>
</ref>
<ref id="B3">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ai]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Yu]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Tan]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Chai]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a Steric-Clashes Alleviating Receptor (SCAR) Strategy]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2016</year>
<volume>56</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1563-75</page-range></nlm-citation>
</ref>
<ref id="B4">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Allen]]></surname>
<given-names><![CDATA[W. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Balius]]></surname>
<given-names><![CDATA[T. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Mukherjee]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Brozell]]></surname>
<given-names><![CDATA[S. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Moustakas]]></surname>
<given-names><![CDATA[D. T.]]></given-names>
</name>
<name>
<surname><![CDATA[Lang]]></surname>
<given-names><![CDATA[P. T.]]></given-names>
</name>
<name>
<surname><![CDATA[Case]]></surname>
<given-names><![CDATA[D. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Kuntz]]></surname>
<given-names><![CDATA[I. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Rizzo]]></surname>
<given-names><![CDATA[R. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[DOCK 6: Impact of new features and current docking performance]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2015</year>
<volume>36</volume>
<numero>15</numero>
<issue>15</issue>
<page-range>1132-56</page-range></nlm-citation>
</ref>
<ref id="B5">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Alogheli]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Olanders]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Schaal]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Brandt]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Karlén]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2017</year>
<volume>57</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>190-202</page-range></nlm-citation>
</ref>
<ref id="B6">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Alonso]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Bliznyuk]]></surname>
<given-names><![CDATA[A. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Gready]]></surname>
<given-names><![CDATA[J. E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Combining docking and molecular dynamic simulations in drug design]]></article-title>
<source><![CDATA[Medicinal Research Reviews]]></source>
<year>2006</year>
<volume>26</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>531-68</page-range></nlm-citation>
</ref>
<ref id="B7">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Altunta&#351;]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Bozkus]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Fraguela]]></surname>
<given-names><![CDATA[B. B.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[GPU accelerated molecular docking simulation with genetic algorithms]]></article-title>
<source><![CDATA[Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)]]></source>
<year>2016</year>
<volume>9598</volume>
<page-range>134-46</page-range><publisher-loc><![CDATA[Springer ]]></publisher-loc>
<publisher-name><![CDATA[Cham]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B8">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Anighoro]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Bajorath]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2016</year>
<volume>56</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>580-7</page-range></nlm-citation>
</ref>
<ref id="B9">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ashtawy]]></surname>
<given-names><![CDATA[H. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Mahapatra]]></surname>
<given-names><![CDATA[N. R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Docking for Drug Discovery: Machine-Learning Approaches for Native Pose Prediction of Protein-Ligand Complexes]]></article-title>
<source><![CDATA[Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)]]></source>
<year>2014</year>
<volume>8452</volume>
<page-range>15-32</page-range><publisher-name><![CDATA[Springer International Publishing]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B10">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Awoonor-Williams]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Walsh]]></surname>
<given-names><![CDATA[A. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Rowley]]></surname>
<given-names><![CDATA[C. N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Modeling covalent-modifier drugs]]></article-title>
<source><![CDATA[Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics]]></source>
<year>2017</year>
<volume>1865</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>1664-75</page-range></nlm-citation>
</ref>
<ref id="B11">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bai]]></surname>
<given-names><![CDATA[F.]]></given-names>
</name>
<name>
<surname><![CDATA[Liao]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Gu]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Jiang]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[An accurate metalloprotein-specific scoring function and molecular docking program devised by a dynamic sampling and iteration optimization strategy]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2015</year>
<volume>55</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>833-47</page-range></nlm-citation>
</ref>
<ref id="B12">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ballester]]></surname>
<given-names><![CDATA[P. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Schreyer]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Blundell]]></surname>
<given-names><![CDATA[T. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2014</year>
<volume>54</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>944-55</page-range></nlm-citation>
</ref>
<ref id="B13">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bansal]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Zheng]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Merz]]></surname>
<given-names><![CDATA[K. M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Incorporation of side chain flexibility into protein binding pockets using MTflex]]></article-title>
<source><![CDATA[Bioorganic and Medicinal Chemistry]]></source>
<year>2016</year>
<volume>24</volume>
<numero>20</numero>
<issue>20</issue>
<page-range>4978-87</page-range></nlm-citation>
</ref>
<ref id="B14">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Barducci]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Bonomi]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Parrinello]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Metadynamics]]></article-title>
<source><![CDATA[Wiley Interdisciplinary Reviews: Computational Molecular Science]]></source>
<year>2011</year>
<volume>1</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>826-43</page-range></nlm-citation>
</ref>
<ref id="B15">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ben-Shimon]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Niv]]></surname>
<given-names><![CDATA[M. Y.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[AnchorDock: Blind and flexible anchor-driven peptide docking]]></article-title>
<source><![CDATA[Structure]]></source>
<year>2015</year>
<volume>23</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>929-40</page-range></nlm-citation>
</ref>
<ref id="B16">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Berman]]></surname>
<given-names><![CDATA[H. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Westbrook]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Feng]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Gilliland]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Bhat]]></surname>
<given-names><![CDATA[T. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Weissig]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Shindyalov]]></surname>
<given-names><![CDATA[I. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Bourne]]></surname>
<given-names><![CDATA[P. E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The protein data bank]]></article-title>
<source><![CDATA[Nucleic Acids Research]]></source>
<year>2000</year>
<volume>28</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>235-42</page-range></nlm-citation>
</ref>
<ref id="B17">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bjerrum]]></surname>
<given-names><![CDATA[E. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Machine learning optimization of cross docking accuracy]]></article-title>
<source><![CDATA[Computational Biology and Chemistry]]></source>
<year>2016</year>
<volume>62</volume>
<page-range>133-44</page-range></nlm-citation>
</ref>
<ref id="B18">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bonvin]]></surname>
<given-names><![CDATA[A. M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Flexible protein-protein docking]]></article-title>
<source><![CDATA[Current Opinion in Structural Biology]]></source>
<year>2006</year>
<volume>16</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>194-200</page-range></nlm-citation>
</ref>
<ref id="B19">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bottegoni]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Kufareva]]></surname>
<given-names><![CDATA[I.]]></given-names>
</name>
<name>
<surname><![CDATA[Totrov]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Abagyan]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2009</year>
<volume>52</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>397-406</page-range></nlm-citation>
</ref>
<ref id="B20">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bozorg-Haddad]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<source><![CDATA[Advanced Optimization by Nature-Inspired Algorithms]]></source>
<year>2018</year>
<volume>720</volume>
<publisher-loc><![CDATA[Singapore ]]></publisher-loc>
<publisher-name><![CDATA[Springer Singapore]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B21">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Brás]]></surname>
<given-names><![CDATA[N. F.]]></given-names>
</name>
<name>
<surname><![CDATA[Cerqueira]]></surname>
<given-names><![CDATA[N. M. F. S. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Sousa]]></surname>
<given-names><![CDATA[S. F.]]></given-names>
</name>
<name>
<surname><![CDATA[Fernandes]]></surname>
<given-names><![CDATA[P. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Ramos]]></surname>
<given-names><![CDATA[M. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Protein ligand docking in drug discovery]]></article-title>
<source><![CDATA[Protein Modelling]]></source>
<year>2014</year>
<publisher-name><![CDATA[Springer]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B22">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Brown]]></surname>
<given-names><![CDATA[C. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Davis]]></surname>
<given-names><![CDATA[H. T.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Receiver operating characteristics curves and related decision measures: A tutorial]]></article-title>
<source><![CDATA[Chemometrics and Intelligent Laboratory Systems]]></source>
<year>2006</year>
<volume>80</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>24-38</page-range></nlm-citation>
</ref>
<ref id="B23">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Cereto-Massagué]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Ojeda]]></surname>
<given-names><![CDATA[M. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Valls]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Mulero]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Pujadas]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Garcia-Vallve]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Tools for in silico target fishing]]></article-title>
<source><![CDATA[Methods]]></source>
<year>2015</year>
<volume>71</volume>
<page-range>98-103</page-range></nlm-citation>
</ref>
<ref id="B24">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Chaput]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Mouawad]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds]]></article-title>
<source><![CDATA[Journal of Cheminformatics]]></source>
<year>2017</year>
<volume>9</volume>
</nlm-citation>
</ref>
<ref id="B25">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Charifson]]></surname>
<given-names><![CDATA[P. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Corkery]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Murcko]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Walters]]></surname>
<given-names><![CDATA[W. P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>1999</year>
<volume>42</volume>
<numero>25</numero>
<issue>25</issue>
<page-range>5100-9</page-range></nlm-citation>
</ref>
<ref id="B26">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Chen]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Menche]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Power]]></surname>
<given-names><![CDATA[T. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Sower]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Peterson]]></surname>
<given-names><![CDATA[J. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Schein]]></surname>
<given-names><![CDATA[C. H.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins]]></article-title>
<source><![CDATA[Proteins: Structure, Function, and Bioinformatics]]></source>
<year>2007</year>
<volume>67</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>593-605</page-range></nlm-citation>
</ref>
<ref id="B27">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Clark]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Tiwary]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Borrelli]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Feng]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Miller]]></surname>
<given-names><![CDATA[E. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Abel]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Friesner]]></surname>
<given-names><![CDATA[R. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Berne]]></surname>
<given-names><![CDATA[B. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations]]></article-title>
<source><![CDATA[Journal of Chemical Theory and Computation]]></source>
<year>2016</year>
<volume>12</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>2990-8</page-range></nlm-citation>
</ref>
<ref id="B28">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Cole]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Davis]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Jones]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Sage]]></surname>
<given-names><![CDATA[C. R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Docking-A Solved Problem?]]></article-title>
<source><![CDATA[Comprehensive Medicinal Chemistry III]]></source>
<year>2017</year>
<page-range>297-318</page-range><publisher-name><![CDATA[Elsevier]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B29">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Corbeil]]></surname>
<given-names><![CDATA[C. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Moitessier]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2009</year>
<volume>49</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>997-1009</page-range></nlm-citation>
</ref>
<ref id="B30">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Craig]]></surname>
<given-names><![CDATA[I. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Essex]]></surname>
<given-names><![CDATA[J. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Spiegel]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Ensemble docking into multiple crystallographically derived protein structures: An evaluation based on the statistical analysis of enrichments]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2010</year>
<volume>50</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>511-24</page-range></nlm-citation>
</ref>
<ref id="B31">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Crawford]]></surname>
<given-names><![CDATA[T. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Tsui]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Flynn]]></surname>
<given-names><![CDATA[E. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Taylor]]></surname>
<given-names><![CDATA[A. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Côté]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Audia]]></surname>
<given-names><![CDATA[J. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Beresini]]></surname>
<given-names><![CDATA[M. H.]]></given-names>
</name>
<name>
<surname><![CDATA[Burdick]]></surname>
<given-names><![CDATA[D. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Cummings]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Dakin]]></surname>
<given-names><![CDATA[L. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Duplessis]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Good]]></surname>
<given-names><![CDATA[A. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Hewitt]]></surname>
<given-names><![CDATA[M. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Jayaram]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Kiefer]]></surname>
<given-names><![CDATA[J. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Jiang]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Murray]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Nasveschuk]]></surname>
<given-names><![CDATA[C. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Pardo]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Poy]]></surname>
<given-names><![CDATA[F.]]></given-names>
</name>
<name>
<surname><![CDATA[Romero]]></surname>
<given-names><![CDATA[F. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Tang]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Zawadzke]]></surname>
<given-names><![CDATA[L. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhu]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Albrecht]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
<name>
<surname><![CDATA[Magnuson]]></surname>
<given-names><![CDATA[S. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Bellon]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Cochran]]></surname>
<given-names><![CDATA[A. G.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2016</year>
<volume>59</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>5391-402</page-range></nlm-citation>
</ref>
<ref id="B32">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Cross]]></surname>
<given-names><![CDATA[J. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Thompson]]></surname>
<given-names><![CDATA[D. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Rai]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
<name>
<surname><![CDATA[Baber]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Fan]]></surname>
<given-names><![CDATA[K. Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Hu]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Humblet]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2009</year>
<volume>49</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>1455-74</page-range></nlm-citation>
</ref>
<ref id="B33">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Da]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Kireev]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Structural Protein-Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2014</year>
<volume>54</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>2555-61</page-range></nlm-citation>
</ref>
<ref id="B34">
<nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dallakyan]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Small-Molecule Library Screening by Docking with PyRx]]></article-title>
<source><![CDATA[Methods in molecular biology (Clifton, N.J.)]]></source>
<year>2015</year>
<volume>1263</volume>
<page-range>243-50</page-range></nlm-citation>
</ref>
<ref id="B35">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dastmalchi]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Dastmalchi]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Hamzeh-Mivehroud]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Sokouti]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
</person-group>
<source><![CDATA[Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery]]></source>
<year>2016</year>
<publisher-name><![CDATA[IGI Global]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B36">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[De Cesco]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Kurian]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Dufresne]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Mittermaier]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Moitessier]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Covalent inhibitors design and discovery]]></article-title>
<source><![CDATA[European Journal of Medicinal Chemistry]]></source>
<year>2017</year>
<volume>138</volume>
<page-range>96-114</page-range></nlm-citation>
</ref>
<ref id="B37">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Debroise]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Shakhnovich]]></surname>
<given-names><![CDATA[E. I.]]></given-names>
</name>
<name>
<surname><![CDATA[Chéron]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2017</year>
<volume>57</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>584-93</page-range></nlm-citation>
</ref>
<ref id="B38">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dhananjayan]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Docking Study Characterization of Rare Flavonoids at the Nac-Binding Site of the First Bromodomain of BRD4 (BRD4 BD1)]]></article-title>
<source><![CDATA[Journal of Cancer Research]]></source>
<year>2015</year>
<volume>2015</volume>
<page-range>1-15</page-range></nlm-citation>
</ref>
<ref id="B39">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dheer]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Jyoti]]></surname>
</name>
<name>
<surname><![CDATA[Gupta]]></surname>
<given-names><![CDATA[P. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Shankar]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Tacrolimus: An updated review on delivering strategies for multifarious diseases]]></article-title>
<source><![CDATA[European Journal of Pharmaceutical Sciences]]></source>
<year>2018</year>
<volume>114</volume>
<page-range>217-27</page-range></nlm-citation>
</ref>
<ref id="B40">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dias]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[de Azevedo Jr.]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Docking Algorithms]]></article-title>
<source><![CDATA[Current Drug Targets]]></source>
<year>2008</year>
<volume>9</volume>
<numero>12</numero>
<issue>12</issue>
<page-range>1040-7</page-range></nlm-citation>
</ref>
<ref id="B41">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Dominguez]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Boelens]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Bonvin]]></surname>
<given-names><![CDATA[A. M. J. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[HADDOCK: A protein-protein docking approach based on biochemical or biophysical information]]></article-title>
<source><![CDATA[Journal of the American Chemical Society]]></source>
<year>2003</year>
<volume>125</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>1731-7</page-range></nlm-citation>
</ref>
<ref id="B42">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Du]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Bleylevens]]></surname>
<given-names><![CDATA[I. W. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Bitorina]]></surname>
<given-names><![CDATA[A. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Wichapong]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Nicolaes]]></surname>
<given-names><![CDATA[G. A. F.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Optimization of compound ranking for structure-based virtual ligand screening using an established FRED-surflex consensus approach]]></article-title>
<source><![CDATA[Chemical Biology and Drug Design]]></source>
<year>2014</year>
<volume>83</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>37-51</page-range></nlm-citation>
</ref>
<ref id="B43">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ehrt]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Brinkjost]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Koch]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2016</year>
<volume>59</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>4121-51</page-range></nlm-citation>
</ref>
<ref id="B44">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Eldridge]]></surname>
<given-names><![CDATA[M. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Murray]]></surname>
<given-names><![CDATA[C. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Auton]]></surname>
<given-names><![CDATA[T. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Paolini]]></surname>
<given-names><![CDATA[G. V]]></given-names>
</name>
<name>
<surname><![CDATA[Mee]]></surname>
<given-names><![CDATA[R. P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>1997</year>
<volume>11</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>425-45</page-range></nlm-citation>
</ref>
<ref id="B45">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ellingson]]></surname>
<given-names><![CDATA[S. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Miao]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Baudry]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Smith]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Multi-conformer ensemble docking to difficult protein targets]]></article-title>
<source><![CDATA[Journal of Physical Chemistry B]]></source>
<year>2015</year>
<volume>119</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>1026-34</page-range></nlm-citation>
</ref>
<ref id="B46">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Elokely]]></surname>
<given-names><![CDATA[K. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Doerksen]]></surname>
<given-names><![CDATA[R. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking challenge: Protein sampling and molecular docking performance]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2013</year>
<volume>53</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1934-45</page-range></nlm-citation>
</ref>
<ref id="B47">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Englebienne]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Moitessier]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2009</year>
<volume>49</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>2564-71</page-range></nlm-citation>
</ref>
<ref id="B48">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ericksen]]></surname>
<given-names><![CDATA[S. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Wu]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhang]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Michael]]></surname>
<given-names><![CDATA[L. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Newton]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Hoffmann]]></surname>
<given-names><![CDATA[F. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Wildman]]></surname>
<given-names><![CDATA[S. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2017</year>
</nlm-citation>
</ref>
<ref id="B49">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Espinoza-Fonseca]]></surname>
<given-names><![CDATA[L. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Trujillo-Ferrara]]></surname>
<given-names><![CDATA[J. G.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Identification of multiple allosteric sites on the M 1 muscarinic acetylcholine receptor]]></article-title>
<source><![CDATA[FEBS Letters]]></source>
<year>2005</year>
<volume>579</volume>
<numero>30</numero>
<issue>30</issue>
<page-range>6726-32</page-range></nlm-citation>
</ref>
<ref id="B50">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Evangelista]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Weir]]></surname>
<given-names><![CDATA[R. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Ellingson]]></surname>
<given-names><![CDATA[S. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Harris]]></surname>
<given-names><![CDATA[J. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Kapoor]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Smith]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Baudry]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Ensemble-based docking: From hit discovery to metabolism and toxicity predictions]]></article-title>
<source><![CDATA[Bioorganic and Medicinal Chemistry]]></source>
<year>2016</year>
<volume>24</volume>
<numero>20</numero>
<issue>20</issue>
<page-range>4928-35</page-range></nlm-citation>
</ref>
<ref id="B51">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ezzat]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Wu]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[X.-L.]]></given-names>
</name>
<name>
<surname><![CDATA[Kwoh]]></surname>
<given-names><![CDATA[C.-K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Drug-target interaction prediction using ensemble learning and dimensionality reduction]]></article-title>
<source><![CDATA[Methods]]></source>
<year>2017</year>
<volume>129</volume>
<page-range>81-8</page-range></nlm-citation>
</ref>
<ref id="B52">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Fakhouri]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[El-Elimat]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Hurst]]></surname>
<given-names><![CDATA[D. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Reggio]]></surname>
<given-names><![CDATA[P. H.]]></given-names>
</name>
<name>
<surname><![CDATA[Pearce]]></surname>
<given-names><![CDATA[C. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Oberlies]]></surname>
<given-names><![CDATA[N. H.]]></given-names>
</name>
<name>
<surname><![CDATA[Croatt]]></surname>
<given-names><![CDATA[M. P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Isolation, semisynthesis, covalent docking and transforming growth factor beta-activated kinase 1 (TAK1)-inhibitory activities of (5Z)-7-oxozeaenol analogues]]></article-title>
<source><![CDATA[Bioorganic and Medicinal Chemistry]]></source>
<year>2015</year>
<volume>23</volume>
<numero>21</numero>
<issue>21</issue>
<page-range>6993-9</page-range></nlm-citation>
</ref>
<ref id="B53">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Fani]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Sattarinezhad]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Bordbar]]></surname>
<given-names><![CDATA[A. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Identification of new 2,5-diketopiperazine derivatives as simultaneous effective inhibitors of &#945;&#946;-tubulin and BCRP proteins: Molecular docking, Structure-Activity Relationships and virtual consensus docking studies]]></article-title>
<source><![CDATA[Journal of Molecular Structure]]></source>
<year>2017</year>
<volume>1137</volume>
<page-range>362-72</page-range></nlm-citation>
</ref>
<ref id="B54">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Feher]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Consensus scoring for protein-ligand interactions]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2006</year>
<volume>11</volume>
<numero>9</numero>
<issue>9</issue>
</nlm-citation>
</ref>
<ref id="B55">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Feher]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Williams]]></surname>
<given-names><![CDATA[C. I.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Numerical errors and chaotic behavior in docking simulations]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2012</year>
<volume>52</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>724-38</page-range></nlm-citation>
</ref>
<ref id="B56">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Feinstein]]></surname>
<given-names><![CDATA[W. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Brylinski]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets]]></article-title>
<source><![CDATA[Feinstein and Brylinski Journal of Cheminformatics]]></source>
<year>2015</year>
<volume>7</volume>
</nlm-citation>
</ref>
<ref id="B57">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ferrari]]></surname>
<given-names><![CDATA[A. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Wei]]></surname>
<given-names><![CDATA[B. Q.]]></given-names>
</name>
<name>
<surname><![CDATA[Costantino]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Shoichet]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Soft docking and multiple receptor conformations in virtual screening]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2004</year>
<volume>47</volume>
<numero>21</numero>
<issue>21</issue>
<page-range>5076-84</page-range></nlm-citation>
</ref>
<ref id="B58">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ferreira]]></surname>
<given-names><![CDATA[L. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Dos Santos]]></surname>
<given-names><![CDATA[R. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Oliva]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Andricopulo]]></surname>
<given-names><![CDATA[A. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular docking and structure-based drug design strategies]]></article-title>
<source><![CDATA[Molecules]]></source>
<year>2015</year>
<volume>20</volume>
</nlm-citation>
</ref>
<ref id="B59">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Fischer]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Merlitz]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Wenzel]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Receptor flexibility for large-scale in silico ligand screens: Chances and challenges]]></article-title>
<source><![CDATA[Methods in Molecular Biology]]></source>
<year>2008</year>
<volume>443</volume>
<page-range>353-64</page-range></nlm-citation>
</ref>
<ref id="B60">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Forli]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Huey]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Pique]]></surname>
<given-names><![CDATA[M. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Sanner]]></surname>
<given-names><![CDATA[M. F.]]></given-names>
</name>
<name>
<surname><![CDATA[Goodsell]]></surname>
<given-names><![CDATA[D. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Computational protein-ligand docking and virtual drug screening with the AutoDock suite]]></article-title>
<source><![CDATA[Nature Protocols]]></source>
<year>2016</year>
<volume>11</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>905-19</page-range></nlm-citation>
</ref>
<ref id="B61">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Friesner]]></surname>
<given-names><![CDATA[R. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Banks]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Murphy]]></surname>
<given-names><![CDATA[R. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Halgren]]></surname>
<given-names><![CDATA[T. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Klicic]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Mainz]]></surname>
<given-names><![CDATA[D. T.]]></given-names>
</name>
<name>
<surname><![CDATA[Repasky]]></surname>
<given-names><![CDATA[M. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Knoll]]></surname>
<given-names><![CDATA[E. H.]]></given-names>
</name>
<name>
<surname><![CDATA[Shelley]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Perry]]></surname>
<given-names><![CDATA[J. K.]]></given-names>
</name>
<name>
<surname><![CDATA[Shaw]]></surname>
<given-names><![CDATA[D. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Francis]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Shenkin]]></surname>
<given-names><![CDATA[P. S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2004</year>
<volume>47</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>1739-49</page-range></nlm-citation>
</ref>
<ref id="B62">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Galdeano]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Ciulli]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology]]></article-title>
<source><![CDATA[Future Medicinal Chemistry]]></source>
<year>2016</year>
<volume>8</volume>
<numero>13</numero>
<issue>13</issue>
<page-range>1655-80</page-range></nlm-citation>
</ref>
<ref id="B63">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Gervasio]]></surname>
<given-names><![CDATA[F. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Laio]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Parrinello]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Flexible docking in solution using metadynamics]]></article-title>
<source><![CDATA[Journal of the American Chemical Society]]></source>
<year>2005</year>
<volume>127</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>2600-7</page-range></nlm-citation>
</ref>
<ref id="B64">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Glover]]></surname>
<given-names><![CDATA[F.]]></given-names>
</name>
<name>
<surname><![CDATA[Sörensen]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Metaheuristics]]></article-title>
<source><![CDATA[Scholarpedia]]></source>
<year>2015</year>
<volume>10</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>6532</page-range></nlm-citation>
</ref>
<ref id="B65">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[González]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Force fields and molecular dynamics simulations]]></article-title>
<source><![CDATA[Collection SFN]]></source>
<year>2011</year>
<volume>12</volume>
<page-range>169-200</page-range></nlm-citation>
</ref>
<ref id="B66">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Goodford]]></surname>
<given-names><![CDATA[P. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>1985</year>
<volume>28</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>849-57</page-range></nlm-citation>
</ref>
<ref id="B67">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Grebner]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Iegre]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Ulander]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Edman]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Hogner]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Tyrchan]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2016</year>
<volume>56</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>774-87</page-range></nlm-citation>
</ref>
<ref id="B68">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Grosan]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Abraham]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Machine Learning]]></article-title>
<source><![CDATA[Intelligent Systems]]></source>
<year>2011</year>
<volume>17</volume>
<page-range>261-8</page-range><publisher-name><![CDATA[Springer International Publishing]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B69">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Grosdidier]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Zoete]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Michielin]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[SwissDock, a protein-small molecule docking web service based on EADock DSS]]></article-title>
<source><![CDATA[Nucleic Acids Research]]></source>
<year>2011</year>
<volume>39</volume>
<numero>SUPPL. 2</numero>
<issue>SUPPL. 2</issue>
</nlm-citation>
</ref>
<ref id="B70">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Grosdidier]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Fernández-Recio]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Identification of hot-spot residues in protein-protein interactions by computational docking]]></article-title>
<source><![CDATA[BMC Bioinformatics]]></source>
<year>2008</year>
<volume>9</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>447</page-range></nlm-citation>
</ref>
<ref id="B71">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Gürsoy]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Smie&#353;ko]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Searching for bioactive conformations of drug-like ligands with current force fields: How good are we?]]></article-title>
<source><![CDATA[Journal of Cheminformatics]]></source>
<year>2017</year>
<volume>9</volume>
<numero>1</numero>
<issue>1</issue>
</nlm-citation>
</ref>
<ref id="B72">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Guvench]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[MacKerell]]></surname>
<given-names><![CDATA[A. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Comparison of Protein Force Fields for Molecular Dynamics Simulations]]></article-title>
<source><![CDATA[Molecular Modeling of Proteins]]></source>
<year>2008</year>
<volume>443</volume>
<page-range>63-88</page-range></nlm-citation>
</ref>
<ref id="B73">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Halperin]]></surname>
<given-names><![CDATA[I.]]></given-names>
</name>
<name>
<surname><![CDATA[Ma]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Wolfson]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Nussinov]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Principles of docking: An overview of search algorithms and a guide to scoring functions]]></article-title>
<source><![CDATA[Proteins: Structure, Function and Genetics]]></source>
<year>2002</year>
<volume>47</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>409-43</page-range></nlm-citation>
</ref>
<ref id="B74">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Harris]]></surname>
<given-names><![CDATA[J. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Eldridge]]></surname>
<given-names><![CDATA[M. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Sayler]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Menn]]></surname>
<given-names><![CDATA[F.-M.]]></given-names>
</name>
<name>
<surname><![CDATA[Layton]]></surname>
<given-names><![CDATA[A. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Baudry]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A computational approach predicting CYP450 metabolism and estrogenic activity of an endocrine disrupting compound (PCB-30)]]></article-title>
<source><![CDATA[Environmental Toxicology and Chemistry]]></source>
<year>2014</year>
<volume>33</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>1615-23</page-range></nlm-citation>
</ref>
<ref id="B75">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Hosta&#353;]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[&#344;ezá&#269;]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Hobza]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions]]></article-title>
<source><![CDATA[Chemical Physics Letters]]></source>
<year>2013</year>
<volume>568-569</volume>
<page-range>161-6</page-range></nlm-citation>
</ref>
<ref id="B76">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Houston]]></surname>
<given-names><![CDATA[D. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Walkinshaw]]></surname>
<given-names><![CDATA[M. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Consensus docking: Improving the reliability of docking in a virtual screening context]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2013</year>
<volume>53</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>384-90</page-range></nlm-citation>
</ref>
<ref id="B77">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Shoichet]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
<name>
<surname><![CDATA[Irwin]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Benchmarking Sets for Molecular Docking]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2006</year>
<volume>49</volume>
<numero>23</numero>
<issue>23</issue>
<page-range>6789-801</page-range></nlm-citation>
</ref>
<ref id="B78">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[S.-Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Grinter]]></surname>
<given-names><![CDATA[S. Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions]]></article-title>
<source><![CDATA[Physical Chemistry Chemical Physics]]></source>
<year>2010</year>
<volume>12</volume>
<numero>40</numero>
<issue>40</issue>
<page-range>12899-908</page-range></nlm-citation>
</ref>
<ref id="B79">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[S. Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking]]></article-title>
<source><![CDATA[Proteins: Structure, Function and Genetics]]></source>
<year>2007</year>
<volume>66</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>399-421</page-range></nlm-citation>
</ref>
<ref id="B80">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Irwin]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Raushel]]></surname>
<given-names><![CDATA[F. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Shoichet]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Virtual Screening against Metalloenzymes for Inhibitors and Substrates]]></article-title>
<source><![CDATA[Biochemistry]]></source>
<year>2005</year>
<volume>44</volume>
<numero>37</numero>
<issue>37</issue>
<page-range>12316-28</page-range></nlm-citation>
</ref>
<ref id="B81">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ishchenko]]></surname>
<given-names><![CDATA[A. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Shakhnovich]]></surname>
<given-names><![CDATA[E. I.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[SMall Molecule Growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2002</year>
<volume>45</volume>
<numero>13</numero>
<issue>13</issue>
<page-range>2770-80</page-range></nlm-citation>
</ref>
<ref id="B82">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Jones]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Willett]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Glen]]></surname>
<given-names><![CDATA[R. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Leach]]></surname>
<given-names><![CDATA[A. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Taylor]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Development and validation of a genetic algorithm for flexible docking]]></article-title>
<source><![CDATA[Journal of Molecular Biology]]></source>
<year>1997</year>
<volume>267</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>727-48</page-range></nlm-citation>
</ref>
<ref id="B83">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Jorgensen]]></surname>
<given-names><![CDATA[W. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Thomas]]></surname>
<given-names><![CDATA[L. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria]]></article-title>
<source><![CDATA[Journal of Chemical Theory and Computation]]></source>
<year>2008</year>
<volume>4</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>869-76</page-range></nlm-citation>
</ref>
<ref id="B84">
<nlm-citation citation-type="confpro">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kannan]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Ganji]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<source><![CDATA[Porting Autodock to CUDA]]></source>
<year>2010</year>
<conf-name><![CDATA[ World Congress on Computational Intelligence]]></conf-name>
<conf-loc> </conf-loc>
<page-range>18-23</page-range></nlm-citation>
</ref>
<ref id="B85">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kapoor]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[McGill]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Peterson]]></surname>
<given-names><![CDATA[C. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Meyers]]></surname>
<given-names><![CDATA[H. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Blackburn]]></surname>
<given-names><![CDATA[M. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Baudry]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2016</year>
<volume>56</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>535-47</page-range></nlm-citation>
</ref>
<ref id="B86">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kelley]]></surname>
<given-names><![CDATA[B. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Brown]]></surname>
<given-names><![CDATA[S. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Warren]]></surname>
<given-names><![CDATA[G. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Muchmore]]></surname>
<given-names><![CDATA[S. W.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[POSIT: Flexible Shape-Guided Docking for Pose Prediction]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2015</year>
<volume>55</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1771-80</page-range></nlm-citation>
</ref>
<ref id="B87">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Khamis]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Gomaa]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Ahmed]]></surname>
<given-names><![CDATA[W. F.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Machine learning in computational docking]]></article-title>
<source><![CDATA[Artificial Intelligence in Medicine]]></source>
<year>2015</year>
</nlm-citation>
</ref>
<ref id="B88">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[King]]></surname>
<given-names><![CDATA[A. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Aaron]]></surname>
<given-names><![CDATA[C. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Organophosphate and Carbamate Poisoning]]></article-title>
<source><![CDATA[Emergency Medicine Clinics of North America]]></source>
<year>2015</year>
</nlm-citation>
</ref>
<ref id="B89">
<nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kitchen]]></surname>
<given-names><![CDATA[D. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Decornez]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Furr]]></surname>
<given-names><![CDATA[J. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Bajorath]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<source><![CDATA[Docking and scoring in virtual screening for drug discovery: methods and applications]]></source>
<year>2004</year>
<volume>3</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>935-49</page-range></nlm-citation>
</ref>
<ref id="B90">
<nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Klausmeyer]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Shipley]]></surname>
<given-names><![CDATA[S. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Zuck]]></surname>
<given-names><![CDATA[K. M.]]></given-names>
</name>
<name>
<surname><![CDATA[McCloud]]></surname>
<given-names><![CDATA[T. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Burkholderia thailandensis]]></surname>
<given-names><![CDATA[Histone deacetylase inhibitors from]]></given-names>
</name>
</person-group>
<source><![CDATA[Journal of Natural Products]]></source>
<year>2011</year>
<volume>74</volume>
<numero>10</numero>
<issue>10</issue>
<page-range>2039-44</page-range></nlm-citation>
</ref>
<ref id="B91">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Knegtel]]></surname>
<given-names><![CDATA[R. M. .]]></given-names>
</name>
<name>
<surname><![CDATA[Kuntz]]></surname>
<given-names><![CDATA[I. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Oshiro]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular docking to ensembles of protein structures]]></article-title>
<source><![CDATA[Journal of Molecular Biology]]></source>
<year>1997</year>
<volume>266</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>424-40</page-range></nlm-citation>
</ref>
<ref id="B92">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Korb]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Olsson]]></surname>
<given-names><![CDATA[T. S. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Bowden]]></surname>
<given-names><![CDATA[S. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Hall]]></surname>
<given-names><![CDATA[R. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Verdonk]]></surname>
<given-names><![CDATA[M. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Liebeschuetz]]></surname>
<given-names><![CDATA[J. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Cole]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Potential and Limitations of Ensemble Docking]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2012</year>
<numero>52</numero>
<issue>52</issue>
<page-range>1262-74</page-range></nlm-citation>
</ref>
<ref id="B93">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Korb]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Stützle]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Exner]]></surname>
<given-names><![CDATA[T. E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Empirical scoring functions for advanced Protein-Ligand docking with PLANTS]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2009</year>
<volume>49</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>84-96</page-range></nlm-citation>
</ref>
<ref id="B94">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kramer]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Rarey]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Lengauer]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking]]></article-title>
<source><![CDATA[Proteins]]></source>
<year>1999</year>
<volume>37</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>228-41</page-range></nlm-citation>
</ref>
<ref id="B95">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Krieger]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Vriend]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[New ways to boost molecular dynamics simulations]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2015</year>
<volume>36</volume>
<numero>13</numero>
<issue>13</issue>
<page-range>996-1007</page-range></nlm-citation>
</ref>
<ref id="B96">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kukol]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Consensus virtual screening approaches to predict protein ligands]]></article-title>
<source><![CDATA[European Journal of Medicinal Chemistry]]></source>
<year>2011</year>
<volume>46</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>4661-4</page-range></nlm-citation>
</ref>
<ref id="B97">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kumalo]]></surname>
<given-names><![CDATA[H. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Bhakat]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Soliman]]></surname>
<given-names><![CDATA[M. E. S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Theory and applications of covalent docking in drug discovery: Merits and pitfalls]]></article-title>
<source><![CDATA[Molecules]]></source>
<year>2015</year>
<volume>20</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>1984-2000</page-range></nlm-citation>
</ref>
<ref id="B98">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kumar]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhang]]></surname>
<given-names><![CDATA[K. Y. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Investigation on the effect of key water molecules on docking performance in CSARdock exercise]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2013</year>
<volume>53</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1880-92</page-range></nlm-citation>
</ref>
<ref id="B99">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kuroda]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Gray]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Pushing the Backbone in Protein-Protein Docking]]></article-title>
<source><![CDATA[Structure]]></source>
<year>2016</year>
<volume>24</volume>
<numero>10</numero>
<issue>10</issue>
<page-range>1821-9</page-range></nlm-citation>
</ref>
<ref id="B100">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lavecchia]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Cerchia]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[In silico methods to address polypharmacology: Current status, applications and future perspectives]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2015</year>
</nlm-citation>
</ref>
<ref id="B101">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lemmon]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Meiler]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Towards Ligand Docking Including Explicit Interface Water Molecules]]></article-title>
<source><![CDATA[PLoS ONE]]></source>
<year>2013</year>
<volume>8</volume>
<numero>6</numero>
<issue>6</issue>
</nlm-citation>
</ref>
<ref id="B102">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Sun]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Du]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Wu]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Cao]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[You]]></surname>
<given-names><![CDATA[Q.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Discovery of novel covalent proteasome inhibitors through a combination of pharmacophore screening, covalent docking, and molecular dynamics simulations]]></article-title>
<source><![CDATA[Journal of Molecular Modeling]]></source>
<year>2014</year>
<volume>20</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>2515</page-range></nlm-citation>
</ref>
<ref id="B103">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lie]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Thomsen]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Pedersen]]></surname>
<given-names><![CDATA[C. N. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Schiøtt]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Christensen]]></surname>
<given-names><![CDATA[M. H.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular docking with ligand attached water molecules]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2011</year>
<volume>51</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>909-17</page-range></nlm-citation>
</ref>
<ref id="B104">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lill]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Multi-dimensional QSAR in drug discovery]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2007</year>
</nlm-citation>
</ref>
<ref id="B105">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[London]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Farelli]]></surname>
<given-names><![CDATA[J. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Brown]]></surname>
<given-names><![CDATA[S. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Korczynska]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Al-Obaidi]]></surname>
<given-names><![CDATA[N. F.]]></given-names>
</name>
<name>
<surname><![CDATA[Babbitt]]></surname>
<given-names><![CDATA[P. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Almo]]></surname>
<given-names><![CDATA[S. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Allen]]></surname>
<given-names><![CDATA[K. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Shoichet]]></surname>
<given-names><![CDATA[B. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases]]></article-title>
<source><![CDATA[Biochemistry]]></source>
<year>2015</year>
<volume>54</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>528-37</page-range></nlm-citation>
</ref>
<ref id="B106">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lopes]]></surname>
<given-names><![CDATA[P. E. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Guvench]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Mackerell]]></surname>
<given-names><![CDATA[A. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Current status of protein force fields for molecular dynamics simulations]]></article-title>
<source><![CDATA[Methods in Molecular Biology]]></source>
<year>2015</year>
<volume>1215</volume>
<page-range>47-71</page-range></nlm-citation>
</ref>
<ref id="B107">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[López-Camacho]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[García Godoy]]></surname>
<given-names><![CDATA[M. J.]]></given-names>
</name>
<name>
<surname><![CDATA[García-Nieto]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Nebro]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Aldana-Montes]]></surname>
<given-names><![CDATA[J. F.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Solving molecular flexible docking problems with metaheuristics: A comparative study]]></article-title>
<source><![CDATA[Applied Soft Computing]]></source>
<year>2015</year>
<volume>28</volume>
<page-range>379-93</page-range></nlm-citation>
</ref>
<ref id="B108">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Madhavi Sastry]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Adzhigirey]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Day]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Annabhimoju]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Sherman]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>2013</year>
<volume>27</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>221-34</page-range></nlm-citation>
</ref>
<ref id="B109">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Marzaro]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Guiotto]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Borgatti]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Finotti]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Gambari]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Breveglieri]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Chilin]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Psoralen derivatives as inhibitors of NF-&#954;B/DNA interaction: Synthesis, molecular modeling, 3D-QSAR, and biological evaluation]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2013</year>
<volume>56</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>1830-42</page-range></nlm-citation>
</ref>
<ref id="B110">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Mccall]]></surname>
<given-names><![CDATA[K. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[C.-C.]]></given-names>
</name>
<name>
<surname><![CDATA[Fierke]]></surname>
<given-names><![CDATA[C. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Zinc and Health: Current Status and Future Directions Function and Mechanism of Zinc Metalloenzymes 1]]></article-title>
<source><![CDATA[J. Nutr]]></source>
<year>2000</year>
<volume>130</volume>
<page-range>1437-46</page-range></nlm-citation>
</ref>
<ref id="B111">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Mcgann]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[FRED Pose Prediction and Virtual Screening Accuracy]]></article-title>
<source><![CDATA[J. Chem. Inf. Model]]></source>
<year>2011</year>
<volume>51</volume>
<page-range>578-96</page-range></nlm-citation>
</ref>
<ref id="B112">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Giulianotti]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Welmaker]]></surname>
<given-names><![CDATA[G. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Houghten]]></surname>
<given-names><![CDATA[R. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Shifting from the single to the multitarget paradigm in drug discovery]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2013</year>
<volume>18</volume>
<numero>9-10</numero>
<issue>9-10</issue>
<page-range>495-501</page-range></nlm-citation>
</ref>
<ref id="B113">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Méndez-Lucio]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Martinez-Mayorga]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The interplay between molecular modeling and chemoinformatics to characterize protein-ligand and protein-protein interactions landscapes for drug discovery]]></article-title>
<source><![CDATA[Advances in Protein Chemistry and Structural Biology]]></source>
<year>2014</year>
<volume>96</volume>
<page-range>1-37</page-range></nlm-citation>
</ref>
<ref id="B114">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Méndez-Lucio]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Naveja]]></surname>
<given-names><![CDATA[J. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Vite-Caritino]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Prieto-Martínez]]></surname>
<given-names><![CDATA[F. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Review. One Drug for Multiple Targets: A Computational Perspective]]></article-title>
<source><![CDATA[J. Mex. Chem. Soc.]]></source>
<year>2016</year>
<volume>60</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>168-81</page-range></nlm-citation>
</ref>
<ref id="B115">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Mendonça]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Barreto]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Guimarães]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Santos]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Pita]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Boratto]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Accelerating Docking Simulation Using Multicore and GPU Systems]]></article-title>
<person-group person-group-type="editor">
<name>
<surname><![CDATA[Gervasi]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Murgante]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Misra]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Borruso]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Torre]]></surname>
<given-names><![CDATA[C. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Rocha]]></surname>
<given-names><![CDATA[A. M. A. C.]]></given-names>
</name>
<name>
<surname><![CDATA[&#8230; Cuzzocrea]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<source><![CDATA[International Conference on Computational Science and Its Applications]]></source>
<year>2017</year>
<volume>10404</volume>
<page-range>439-51</page-range><publisher-loc><![CDATA[Cham ]]></publisher-loc>
<publisher-name><![CDATA[Springer International Publishing]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B116">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Meng]]></surname>
<given-names><![CDATA[X.-Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhang]]></surname>
<given-names><![CDATA[H.-X.]]></given-names>
</name>
<name>
<surname><![CDATA[Mezei]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Cui]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular docking: a powerful approach for structure-based drug discovery]]></article-title>
<source><![CDATA[Current Computer-Aided Drug Design]]></source>
<year>2011</year>
<volume>7</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>146-57</page-range></nlm-citation>
</ref>
<ref id="B117">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Moitessier]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Pottel]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Therrien]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Englebienne]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Tomberg]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Corbeil]]></surname>
<given-names><![CDATA[C. R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Medicinal Chemistry Projects Requiring Imaginative Structure -Based Drug Design Methods]]></article-title>
<source><![CDATA[Accounts of Chemical Research]]></source>
<year>2016</year>
<volume>49</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>1646-57</page-range></nlm-citation>
</ref>
<ref id="B118">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Monticelli]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Tieleman]]></surname>
<given-names><![CDATA[D. P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Force fields for classical molecular dynamics]]></article-title>
<source><![CDATA[Methods in Molecular Biology]]></source>
<year>2013</year>
<volume>924</volume>
<page-range>197-213</page-range></nlm-citation>
</ref>
<ref id="B119">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Morris]]></surname>
<given-names><![CDATA[G. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Lim-Wilby]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Docking]]></article-title>
<source><![CDATA[Methods in molecular biology]]></source>
<year>2008</year>
<volume>443</volume>
<page-range>365-82</page-range></nlm-citation>
</ref>
<ref id="B120">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Morris]]></surname>
<given-names><![CDATA[G. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Ruth]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Lindstrom]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Sanner]]></surname>
<given-names><![CDATA[M. F.]]></given-names>
</name>
<name>
<surname><![CDATA[Belew]]></surname>
<given-names><![CDATA[R. K.]]></given-names>
</name>
<name>
<surname><![CDATA[Goodsell]]></surname>
<given-names><![CDATA[D. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2009</year>
<volume>30</volume>
<numero>16</numero>
<issue>16</issue>
<page-range>2785-91</page-range></nlm-citation>
</ref>
<ref id="B121">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Motta]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Bonati]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2017</year>
</nlm-citation>
</ref>
<ref id="B122">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Muegge]]></surname>
<given-names><![CDATA[I.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A knowledge-based scoring function for protein-ligand interactions: Probing the reference state]]></article-title>
<source><![CDATA[Perspectives in Drug Discovery and Design]]></source>
<year>2000</year>
<volume>20</volume>
<page-range>99-114</page-range></nlm-citation>
</ref>
<ref id="B123">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Murphy]]></surname>
<given-names><![CDATA[R. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Repasky]]></surname>
<given-names><![CDATA[M. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Greenwood]]></surname>
<given-names><![CDATA[J. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Tubert-Brohman]]></surname>
<given-names><![CDATA[I.]]></given-names>
</name>
<name>
<surname><![CDATA[Jerome]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Annabhimoju]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Boyles]]></surname>
<given-names><![CDATA[N. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Schmitz]]></surname>
<given-names><![CDATA[C. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Abel]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Farid]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Friesner]]></surname>
<given-names><![CDATA[R. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2016</year>
<volume>59</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>4364-84</page-range></nlm-citation>
</ref>
<ref id="B124">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Murray]]></surname>
<given-names><![CDATA[C. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Auton]]></surname>
<given-names><![CDATA[T. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Eldridge]]></surname>
<given-names><![CDATA[M. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>1998</year>
<volume>12</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>503-19</page-range></nlm-citation>
</ref>
<ref id="B125">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Nabuurs]]></surname>
<given-names><![CDATA[S. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Wagener]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[De Vlieg]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A flexible approach to induced fit docking]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2007</year>
<volume>50</volume>
<numero>26</numero>
<issue>26</issue>
<page-range>6507-18</page-range></nlm-citation>
</ref>
<ref id="B126">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Neves]]></surname>
<given-names><![CDATA[M. A. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Totrov]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Abagyan]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking and scoring with ICM: The benchmarking results and strategies for improvement]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>2012</year>
<volume>26</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>675-86</page-range></nlm-citation>
</ref>
<ref id="B127">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Nikitina]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Sulimov]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Zayets]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Zaitseva]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Semiempirical Calculations of Binding Enthalpy for Protein-Ligand Complexes]]></article-title>
<source><![CDATA[International Journal of Quantum Chemistry]]></source>
<year>2004</year>
<volume>97</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>747-63</page-range></nlm-citation>
</ref>
<ref id="B128">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Oferkin]]></surname>
<given-names><![CDATA[I. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Katkova]]></surname>
<given-names><![CDATA[E. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Sulimov]]></surname>
<given-names><![CDATA[A. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Kutov]]></surname>
<given-names><![CDATA[D. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Sobolev]]></surname>
<given-names><![CDATA[S. I.]]></given-names>
</name>
<name>
<surname><![CDATA[Voevodin]]></surname>
<given-names><![CDATA[V. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Sulimov]]></surname>
<given-names><![CDATA[V. B.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima]]></article-title>
<source><![CDATA[Advances in Bioinformatics]]></source>
<year>2015</year>
<volume>2015</volume>
<page-range>1-12</page-range></nlm-citation>
</ref>
<ref id="B129">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ohno]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Kamiya]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Asakawa]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Inoue]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Sakurai]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Application of an integrated MOZYME+DFT method to pKa calculations for proteins]]></article-title>
<source><![CDATA[Chemical Physics Letters]]></source>
<year>2001</year>
<volume>341</volume>
<numero>3-4</numero>
<issue>3-4</issue>
<page-range>387-92</page-range></nlm-citation>
</ref>
<ref id="B130">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Onawole]]></surname>
<given-names><![CDATA[A. T.]]></given-names>
</name>
<name>
<surname><![CDATA[Sulaiman]]></surname>
<given-names><![CDATA[K. O.]]></given-names>
</name>
<name>
<surname><![CDATA[Adegoke]]></surname>
<given-names><![CDATA[R. O.]]></given-names>
</name>
<name>
<surname><![CDATA[Kolapo]]></surname>
<given-names><![CDATA[T. U.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Identification of potential inhibitors against the Zika virus using consensus scoring]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2017</year>
<volume>73</volume>
<page-range>54-61</page-range></nlm-citation>
</ref>
<ref id="B131">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Parikh]]></surname>
<given-names><![CDATA[H. I.]]></given-names>
</name>
<name>
<surname><![CDATA[Kellogg]]></surname>
<given-names><![CDATA[G. E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality]]></article-title>
<source><![CDATA[Proteins:Structure, Function and Bioinformatics]]></source>
<year>2014</year>
<volume>82</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>916-32</page-range></nlm-citation>
</ref>
<ref id="B132">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Park]]></surname>
<given-names><![CDATA[S. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Kufareva]]></surname>
<given-names><![CDATA[I.]]></given-names>
</name>
<name>
<surname><![CDATA[Abagyan]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>2010</year>
<volume>24</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>459-71</page-range></nlm-citation>
</ref>
<ref id="B133">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Pason]]></surname>
<given-names><![CDATA[L. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Sotriffer]]></surname>
<given-names><![CDATA[C. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Empirical Scoring Functions for Affinity Prediction of Protein-ligand Complexes]]></article-title>
<source><![CDATA[Molecular Informatics]]></source>
<year>2016</year>
<volume>35</volume>
<numero>11-12</numero>
<issue>11-12</issue>
<page-range>541-8</page-range></nlm-citation>
</ref>
<ref id="B134">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Paul]]></surname>
<given-names><![CDATA[D. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Gautham]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[iMOLSDOCK: Induced-fit docking using mutually orthogonal Latin squares (MOLS)]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2017</year>
<volume>74</volume>
<page-range>89-99</page-range></nlm-citation>
</ref>
<ref id="B135">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Pedretti]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Villa]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Vistoli]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>2004</year>
<volume>18</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>167-73</page-range></nlm-citation>
</ref>
<ref id="B136">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Perola]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
<name>
<surname><![CDATA[Walters]]></surname>
<given-names><![CDATA[W. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Charifson]]></surname>
<given-names><![CDATA[P. S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance]]></article-title>
<source><![CDATA[Proteins: Structure, Function and Genetics]]></source>
<year>2004</year>
<volume>56</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>235-49</page-range></nlm-citation>
</ref>
<ref id="B137">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Plewczynski]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[&#321;a&#380;niewski]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Grotthuss]]></surname>
<given-names><![CDATA[M. Von]]></given-names>
</name>
<name>
<surname><![CDATA[Rychlewski]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Ginalski]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[VoteDock: Consensus docking method for prediction of protein-ligand interactions]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2011</year>
<volume>32</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>568-81</page-range></nlm-citation>
</ref>
<ref id="B138">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Prieto-Martínez]]></surname>
<given-names><![CDATA[F. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Charting the Bromodomain BRD4: Towards the Identification of Novel Inhibitors with Molecular Similarity and Receptor Mapping]]></article-title>
<source><![CDATA[Letters in Drug Design &amp; Discovery]]></source>
<year>2018</year>
<volume>14</volume>
</nlm-citation>
</ref>
<ref id="B139">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ramírez]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Caballero]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Is it reliable to use common molecular docking methods for comparing the binding affinities of enantiomer pairs for their protein target?]]></article-title>
<source><![CDATA[International Journal of Molecular Sciences]]></source>
<year>2016</year>
<volume>17</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>1-15</page-range></nlm-citation>
</ref>
<ref id="B140">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ran]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhang]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Lu]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Xiong]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhang]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Lu]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Lu]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Chen]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Insight into the key interactions of bromodomain inhibitors based on molecular docking, interaction fingerprinting, molecular dynamics and binding free energy calculation]]></article-title>
<source><![CDATA[Molecular bioSystems]]></source>
<year>2015</year>
<volume>11</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>1295-304</page-range></nlm-citation>
</ref>
<ref id="B141">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Roberts]]></surname>
<given-names><![CDATA[B. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Mancera]]></surname>
<given-names><![CDATA[R. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Ligand-protein docking with water molecules]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2008</year>
<volume>48</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>397-408</page-range></nlm-citation>
</ref>
<ref id="B142">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ross]]></surname>
<given-names><![CDATA[G. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Morris]]></surname>
<given-names><![CDATA[G. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Biggin]]></surname>
<given-names><![CDATA[P. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Rapid and accurate prediction and scoring of water molecules in protein binding sites]]></article-title>
<source><![CDATA[PLoS ONE]]></source>
<year>2012</year>
<volume>7</volume>
<numero>3</numero>
<issue>3</issue>
</nlm-citation>
</ref>
<ref id="B143">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ruiz-Carmona]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Alvarez-Garcia]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Foloppe]]></surname>
<given-names><![CDATA[N.]]></given-names>
</name>
<name>
<surname><![CDATA[Garmendia-Doval]]></surname>
<given-names><![CDATA[A. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Juhos]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Schmidtke]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Barril]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Hubbard]]></surname>
<given-names><![CDATA[R. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Morley]]></surname>
<given-names><![CDATA[S. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids]]></article-title>
<source><![CDATA[PLoS Computational Biology]]></source>
<year>2014</year>
<volume>10</volume>
<numero>4</numero>
<issue>4</issue>
</nlm-citation>
</ref>
<ref id="B144">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sacquin-Mora]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Prévost]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking Peptides on Proteins: How to open a lock, in the dark, with a flexible key]]></article-title>
<source><![CDATA[Structure]]></source>
<year>2015</year>
<volume>23</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1373-4</page-range></nlm-citation>
</ref>
<ref id="B145">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Saldívar-González]]></surname>
<given-names><![CDATA[F. I.]]></given-names>
</name>
<name>
<surname><![CDATA[Prieto-Martínez]]></surname>
<given-names><![CDATA[F. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[J. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Descubrimiento y desarrollo de fármacos: un enfoque computacional]]></article-title>
<source><![CDATA[Educación Química]]></source>
<year>2017</year>
<volume>28</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>51-8</page-range></nlm-citation>
</ref>
<ref id="B146">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Samanta]]></surname>
<given-names><![CDATA[P. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Das]]></surname>
<given-names><![CDATA[K. K.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2017</year>
<volume>75</volume>
<page-range>294-305</page-range></nlm-citation>
</ref>
<ref id="B147">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Santos-Martins]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Forli]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Ramos]]></surname>
<given-names><![CDATA[M. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[AutoDock4 Zn : An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2014</year>
<volume>54</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>2371-9</page-range></nlm-citation>
</ref>
<ref id="B148">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Scholz]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Knorr]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Hamacher]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Schmidt]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[DOCKTITE-A highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2015</year>
<volume>55</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>398-406</page-range></nlm-citation>
</ref>
<ref id="B149">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Schröder]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Klinger]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Oellien]]></surname>
<given-names><![CDATA[F.]]></given-names>
</name>
<name>
<surname><![CDATA[Marhöfer]]></surname>
<given-names><![CDATA[R. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Duszenko]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Selzer]]></surname>
<given-names><![CDATA[P. M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Docking-based virtual screening of covalently binding ligands: An orthogonal lead discovery approach]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2013</year>
<volume>56</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>1478-90</page-range></nlm-citation>
</ref>
<ref id="B150">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Senter]]></surname>
<given-names><![CDATA[P. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Sievers]]></surname>
<given-names><![CDATA[E. L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The discovery and development of brentuximab vedotin for use in relapsed Hodgkin lymphoma and systemic anaplastic large cell lymphoma]]></article-title>
<source><![CDATA[Nature Biotechnology]]></source>
<year>2012</year>
<volume>30</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>631-7</page-range></nlm-citation>
</ref>
<ref id="B151">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sheng]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Chen]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Liu]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Tang]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2014</year>
<volume>54</volume>
<page-range>90-9</page-range></nlm-citation>
</ref>
<ref id="B152">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sørensen]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Demir]]></surname>
<given-names><![CDATA[Ö.]]></given-names>
</name>
<name>
<surname><![CDATA[Swift]]></surname>
<given-names><![CDATA[R. V]]></given-names>
</name>
<name>
<surname><![CDATA[Feher]]></surname>
<given-names><![CDATA[V. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Amaro]]></surname>
<given-names><![CDATA[R. E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular docking to flexible targets]]></article-title>
<source><![CDATA[Molecular Modeling of Proteins: Second Edition]]></source>
<year>2014</year>
<volume>1215</volume>
<page-range>445-69</page-range></nlm-citation>
</ref>
<ref id="B153">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Spitzer]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Jain]]></surname>
<given-names><![CDATA[A. N.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Surflex-Dock: Docking benchmarks and real-world application]]></article-title>
<source><![CDATA[Journal of Computer-Aided Molecular Design]]></source>
<year>2012</year>
<volume>26</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>687-99</page-range></nlm-citation>
</ref>
<ref id="B154">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sridhar]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Ross]]></surname>
<given-names><![CDATA[G. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Biggin]]></surname>
<given-names><![CDATA[P. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Ward]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Pardo]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Mortenson]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin]]></article-title>
<source><![CDATA[PLOS ONE]]></source>
<year>2017</year>
<volume>12</volume>
<numero>2</numero>
<issue>2</issue>
</nlm-citation>
</ref>
<ref id="B155">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Stank]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Kokh]]></surname>
<given-names><![CDATA[D. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Fuller]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Wade]]></surname>
<given-names><![CDATA[R. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Protein Binding Pocket Dynamics]]></article-title>
<source><![CDATA[Accounts of Chemical Research]]></source>
<year>2016</year>
<volume>49</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>809-15</page-range></nlm-citation>
</ref>
<ref id="B156">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Stewart]]></surname>
<given-names><![CDATA[J. J. P.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Application of the PM6 method to modeling the solid state]]></article-title>
<source><![CDATA[Journal of Molecular Modeling]]></source>
<year>2008</year>
<volume>14</volume>
<numero>6</numero>
<issue>6</issue>
<page-range>499-535</page-range></nlm-citation>
</ref>
<ref id="B157">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sulimov]]></surname>
<given-names><![CDATA[A. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Kutov]]></surname>
<given-names><![CDATA[D. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Katkova]]></surname>
<given-names><![CDATA[E. V.]]></given-names>
</name>
<name>
<surname><![CDATA[Ilin]]></surname>
<given-names><![CDATA[I. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Sulimov]]></surname>
<given-names><![CDATA[V. B.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2017</year>
<volume>78</volume>
<page-range>139-47</page-range></nlm-citation>
</ref>
<ref id="B158">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Toledo Warshaviak]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Golan]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Borrelli]]></surname>
<given-names><![CDATA[K. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhu]]></surname>
<given-names><![CDATA[K.]]></given-names>
</name>
<name>
<surname><![CDATA[Kalid]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Structure-based virtual screening approach for discovery of covalently bound ligands]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2014</year>
<volume>54</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>1941-50</page-range></nlm-citation>
</ref>
<ref id="B159">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Trott]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2009</year>
<volume>31</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>NA</page-range></nlm-citation>
</ref>
<ref id="B160">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Tuccinardi]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Poli]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Romboli]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Giordano]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Martinelli]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2014</year>
<volume>54</volume>
<numero>10</numero>
<issue>10</issue>
<page-range>2980-6</page-range></nlm-citation>
</ref>
<ref id="B161">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Uehara]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Tanaka]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[AutoDock-GIST: Incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking]]></article-title>
<source><![CDATA[Molecules]]></source>
<year>2016</year>
<volume>21</volume>
<numero>11</numero>
<issue>11</issue>
</nlm-citation>
</ref>
<ref id="B162">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Uehara]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Tanaka]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations]]></article-title>
<source><![CDATA[Journal of Chemical Information and Modeling]]></source>
<year>2017</year>
<volume>57</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>742-56</page-range></nlm-citation>
</ref>
<ref id="B163">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Unzue]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhao]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Lolli]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Dong]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhu]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Zechner]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Dolbois]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Caflisch]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Nevado]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The &#8220;gatekeeper&#8221; Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2016</year>
<volume>59</volume>
<numero>7</numero>
<issue>7</issue>
<page-range>3087-97</page-range></nlm-citation>
</ref>
<ref id="B164">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vahl Quevedo]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[De Paris]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[D. Ruiz]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Norberto De Souza]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A strategic solution to optimize molecular docking simulations using Fully-Flexible Receptor models]]></article-title>
<source><![CDATA[Expert Systems with Applications]]></source>
<year>2014</year>
<volume>41</volume>
<numero>16</numero>
<issue>16</issue>
<page-range>7608-20</page-range></nlm-citation>
</ref>
<ref id="B165">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vakser]]></surname>
<given-names><![CDATA[I. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Protein-protein docking: From interaction to interactome]]></article-title>
<source><![CDATA[Biophysical Journal]]></source>
<year>2014</year>
<volume>107</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>1785-93</page-range></nlm-citation>
</ref>
<ref id="B166">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[VanderMolen]]></surname>
<given-names><![CDATA[K. M.]]></given-names>
</name>
<name>
<surname><![CDATA[McCulloch]]></surname>
<given-names><![CDATA[W.]]></given-names>
</name>
<name>
<surname><![CDATA[Pearce]]></surname>
<given-names><![CDATA[C. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Oberlies]]></surname>
<given-names><![CDATA[N. H.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Romidepsin (Istodax, NSC 630176, FR901228, FK228, depsipeptide): a natural product recently approved for cutaneous T-cell lymphoma]]></article-title>
<source><![CDATA[The Journal of Antibiotics]]></source>
<year>2011</year>
<volume>64</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>525-31</page-range></nlm-citation>
</ref>
<ref id="B167">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Venkatachalam]]></surname>
<given-names><![CDATA[C. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Jiang]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Oldfield]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Waldman]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites]]></article-title>
<source><![CDATA[Journal of Molecular Graphics and Modelling]]></source>
<year>2003</year>
<volume>21</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>289-307</page-range></nlm-citation>
</ref>
<ref id="B168">
<nlm-citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Verdonk]]></surname>
<given-names><![CDATA[M. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Taylor]]></surname>
<given-names><![CDATA[R. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Chessari]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Murray]]></surname>
<given-names><![CDATA[C. W.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Illustration of Current Challenges in Molecular Docking]]></article-title>
<source><![CDATA[Structure-Based Drug Discovery]]></source>
<year>2007</year>
<page-range>201-21</page-range><publisher-loc><![CDATA[Dordrecht ]]></publisher-loc>
<publisher-name><![CDATA[Springer Netherlands]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B169">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vilar]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Costanzi]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Application of Monte Carlo-based receptor ensemble docking to virtual screening for GPCR ligands]]></article-title>
<source><![CDATA[Methods in Enzymology]]></source>
<year>2013</year>
<volume>522</volume>
<page-range>263-78</page-range></nlm-citation>
</ref>
<ref id="B170">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vilar]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Cozza]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Moro]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery]]></article-title>
<source><![CDATA[Current Topics in Medicinal Chemistry]]></source>
<year>2008</year>
<volume>8</volume>
<numero>18</numero>
<issue>18</issue>
<page-range>1555-72</page-range></nlm-citation>
</ref>
<ref id="B171">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vreven]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Moal]]></surname>
<given-names><![CDATA[I. H.]]></given-names>
</name>
<name>
<surname><![CDATA[Vangone]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Pierce]]></surname>
<given-names><![CDATA[B. G.]]></given-names>
</name>
<name>
<surname><![CDATA[Kastritis]]></surname>
<given-names><![CDATA[P. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Torchala]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Chaleil]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Jiménez-García]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Bates]]></surname>
<given-names><![CDATA[P. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Fernandez-Recio]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Bonvin]]></surname>
<given-names><![CDATA[A. M. M. J. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Weng]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2]]></article-title>
<source><![CDATA[Journal of Molecular Biology]]></source>
<year>2015</year>
<volume>427</volume>
<numero>19</numero>
<issue>19</issue>
<page-range>3031-41</page-range></nlm-citation>
</ref>
<ref id="B172">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wada]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Sakurai]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A quantum chemical method for rapid optimization of protein structures]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2005</year>
<volume>26</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>160-8</page-range></nlm-citation>
</ref>
<ref id="B173">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wagener]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Ve Vlieg]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Nabuurs]]></surname>
<given-names><![CDATA[S. B.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Flexible protein-ligand docking using the fleksy protocol]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2012</year>
<volume>33</volume>
<numero>12</numero>
<issue>12</issue>
<page-range>1215-7</page-range></nlm-citation>
</ref>
<ref id="B174">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Bradley]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Baker]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Protein-Protein Docking with Backbone Flexibility]]></article-title>
<source><![CDATA[Journal of Molecular Biology]]></source>
<year>2007</year>
<volume>373</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>503-19</page-range></nlm-citation>
</ref>
<ref id="B175">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Lu]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Comparative evaluation of 11 scoring functions for molecular docking]]></article-title>
<source><![CDATA[Journal of Medicinal Chemistry]]></source>
<year>2003</year>
<volume>46</volume>
<numero>12</numero>
<issue>12</issue>
<page-range>2287-303</page-range></nlm-citation>
</ref>
<ref id="B176">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[R.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[How does consensus scoring work for virtual library screening? An idealized computer experiment]]></article-title>
<source><![CDATA[Journal of Chemical Information and Computer Sciences]]></source>
<year>2001</year>
<volume>41</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>1422-6</page-range></nlm-citation>
</ref>
<ref id="B177">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Sun]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Yao]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Li.]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Tian]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Hou]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power]]></article-title>
<source><![CDATA[Physical Chemistry Chemical Physics: PCCP]]></source>
<year>2016</year>
<volume>18</volume>
<page-range>12964-75</page-range></nlm-citation>
</ref>
<ref id="B178">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Warren]]></surname>
<given-names><![CDATA[G. L.]]></given-names>
</name>
<name>
<surname><![CDATA[Do]]></surname>
<given-names><![CDATA[T. D.]]></given-names>
</name>
<name>
<surname><![CDATA[Kelley]]></surname>
<given-names><![CDATA[B. P.]]></given-names>
</name>
<name>
<surname><![CDATA[Nicholls]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Warren]]></surname>
<given-names><![CDATA[S. D.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Essential considerations for using protein-ligand structures in drug discovery]]></article-title>
<source><![CDATA[Drug Discovery Today]]></source>
<year>2012</year>
<volume>17</volume>
<numero>23-24</numero>
<issue>23-24</issue>
<page-range>1270-81</page-range></nlm-citation>
</ref>
<ref id="B179">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Waszkowycz]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Clark]]></surname>
<given-names><![CDATA[D. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Gancia]]></surname>
<given-names><![CDATA[E.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Outstanding challenges in protein-ligand docking and structure-based virtual screening]]></article-title>
<source><![CDATA[Wiley Interdisciplinary Reviews: Computational Molecular Science]]></source>
<year>2011</year>
<volume>1</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>229-59</page-range></nlm-citation>
</ref>
<ref id="B180">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Lill]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Induced fit docking, and the use of QM/MM methods in docking]]></article-title>
<source><![CDATA[Drug Discovery Today: Technologies]]></source>
<year>2013</year>
</nlm-citation>
</ref>
<ref id="B181">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Yan]]></surname>
<given-names><![CDATA[C.]]></given-names>
</name>
<name>
<surname><![CDATA[Xu]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[X.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction]]></article-title>
<source><![CDATA[Structure]]></source>
<year>2016</year>
<volume>24</volume>
<numero>10</numero>
<issue>10</issue>
<page-range>1842-53</page-range></nlm-citation>
</ref>
<ref id="B182">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Yang]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Zhou]]></surname>
<given-names><![CDATA[Q.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[Y.]]></given-names>
</name>
<name>
<surname><![CDATA[Luan]]></surname>
<given-names><![CDATA[Z.]]></given-names>
</name>
<name>
<surname><![CDATA[Qian]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Li]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[GPU Acceleration of Dock6&#8217;s Amber Scoring Computation]]></article-title>
<source><![CDATA[Advances in experimental medicine and biology]]></source>
<year>2010</year>
<volume>680</volume>
<page-range>497-511</page-range></nlm-citation>
</ref>
<ref id="B183">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Yang]]></surname>
<given-names><![CDATA[J. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Chen]]></surname>
<given-names><![CDATA[C. C.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[GEMDOCK: A Generic Evolutionary Method for Molecular Docking]]></article-title>
<source><![CDATA[Proteins: Structure, Function and Genetics]]></source>
<year>2004</year>
<volume>55</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>288-304</page-range></nlm-citation>
</ref>
<ref id="B184">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Zhao]]></surname>
<given-names><![CDATA[H.]]></given-names>
</name>
<name>
<surname><![CDATA[Gartenmann]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
<name>
<surname><![CDATA[Dong]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Spiliotopoulos]]></surname>
<given-names><![CDATA[D.]]></given-names>
</name>
<name>
<surname><![CDATA[Caflisch]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking]]></article-title>
<source><![CDATA[Bioorganic and Medicinal Chemistry Letters]]></source>
<year>2014</year>
<volume>24</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>2493-6</page-range></nlm-citation>
</ref>
<ref id="B185">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Zoete]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Cuendet]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Grosdidier]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Michielin]]></surname>
<given-names><![CDATA[O.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[SwissParam: A fast force field generation tool for small organic molecules]]></article-title>
<source><![CDATA[Journal of Computational Chemistry]]></source>
<year>2011</year>
<volume>32</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>2359-68</page-range></nlm-citation>
</ref>
<ref id="B186">
<nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[K. H.]]></given-names>
</name>
<name>
<surname><![CDATA[O&#8217;Malley]]></surname>
<given-names><![CDATA[A. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Mauri]]></surname>
<given-names><![CDATA[L.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Receiver-Operating Characteristic Analysis for Evaluating Diagnostic Tests and Predictive Models]]></article-title>
<source><![CDATA[Circulation]]></source>
<year>2007</year>
<volume>115</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>654</page-range></nlm-citation>
</ref>
</ref-list>
</back>
</article>
