{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T08:02:51Z","timestamp":1777104171191,"version":"3.51.4"},"reference-count":91,"publisher":"Elsevier","isbn-type":[{"value":"9780128114322","type":"print"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20275-6","type":"book-chapter","created":{"date-parts":[[2018,4,23]],"date-time":"2018-04-23T04:21:49Z","timestamp":1524457309000},"page":"585-600","source":"Crossref","is-referenced-by-count":10,"title":["Rational Structure-Based Drug Design"],"prefix":"10.1016","author":[{"given":"Varun","family":"Khanna","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shoba","family":"Ranganathan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolai","family":"Petrovsky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib1","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1021\/cr040426m","article-title":"Molecular dynamics: Survey of methods for simulating the activity of proteins","volume":"106","author":"Adcock","year":"2006","journal-title":"Chem. Rev."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib2","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1002\/jcc.23905","article-title":"DOCK 6: Impact of new features and current docking performance","volume":"36","author":"Allen","year":"2015","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib3","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"Anfinsen","year":"1973","journal-title":"Science"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib4","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/nature12876","article-title":"A molecular marker of artemisinin-resistant Plasmodium falciparum malaria","volume":"505","author":"Ariey","year":"2014","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10969-008-9048-5","article-title":"The protein model portal","volume":"10","author":"Arnold","year":"2009","journal-title":"J. Struct. Funct. Genomics"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib6","doi-asserted-by":"crossref","first-page":"2719","DOI":"10.1021\/jm901137j","article-title":"New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays","volume":"53","author":"Baell","year":"2010","journal-title":"J. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib7","doi-asserted-by":"crossref","first-page":"D1083","DOI":"10.1093\/nar\/gkt1031","article-title":"The ChEMBL bioactivity database: An update","volume":"42","author":"Bento","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib8","doi-asserted-by":"crossref","first-page":"9763","DOI":"10.1021\/jm301008n","article-title":"Rules for identifying potentially reactive or promiscuous compounds","volume":"55","author":"Bruns","year":"2012","journal-title":"J. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib9","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1023\/A:1016366013656","article-title":"Modified AutoDock for accurate docking of protein kinase inhibitors","volume":"16","author":"Buzko","year":"2002","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib10","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/bioinformatics\/btn307","article-title":"ChemmineR: A compound mining framework for R","volume":"24","author":"Cao","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib11","doi-asserted-by":"crossref","first-page":"e1000585","DOI":"10.1371\/journal.pcbi.1000585","article-title":"Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure","volume":"5","author":"Capra","year":"2009","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib12","doi-asserted-by":"crossref","first-page":"5100","DOI":"10.1021\/jm990352k","article-title":"Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins","volume":"42","author":"Charifson","year":"1999","journal-title":"J. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib13","unstructured":"ChemAxon \u2013 Software for Chemistry and Biology, 2017. (WWW Document). ChemAxon \u2013 Softw. Chem. Biol. RD. Available at: https:\/\/www.chemaxon.com\/ (accessed 09.11.17)."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib14","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1002\/j.1460-2075.1986.tb04288.x","article-title":"The relation between the divergence of sequence and structure in proteins","volume":"5","author":"Chothia","year":"1986","journal-title":"EMBO J."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib15","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1021\/ci900056c","article-title":"Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy","volume":"49","author":"Cross","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib16","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/j.chembiol.2014.08.013","article-title":"Oral druggable space beyond the rule of 5: Insights from drugs and clinical candidates","volume":"21","author":"Doak","year":"2014","journal-title":"Chem. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib87","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: A protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib17","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1006\/jmbi.1993.1170","article-title":"Backbone-dependent rotamer library for proteins. Application to side-chain prediction","volume":"230","author":"Dunbrack","year":"1993","journal-title":"J. Mol. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib18","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1002\/med.20082","article-title":"Plasmepsins as potential targets for new antimalarial therapy","volume":"26","author":"Ersmark","year":"2006","journal-title":"Med. Res. Rev."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib19","doi-asserted-by":"crossref","unstructured":"Eswar, N., Webb, B., Marti-Renom, M.A., et al., 2006. Comparative Protein Structure Modeling Using Modeller. Curr. Protoc. Bioinforma. Ed. Board Andreas Baxevanis Al 0 5, Unit-5.6. Available at: https:\/\/doi.org\/10.1002\/0471250953.bi0506s15.","DOI":"10.1002\/0471250953.bi0506s15"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib20","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/465297a","article-title":"Drug discovery: Priming the antimalarial pipeline","volume":"465","author":"Fidock","year":"2010","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib21","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S0076-6879(03)74020-8","article-title":"Modeller: Generation and refinement of homology-based protein structure models","volume":"374","author":"Fiser","year":"2003","journal-title":"Methods Enzymol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib81","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1038\/nprot.2016.051","article-title":"Computational protein-ligand docking and virtual drug screening with the AutoDock suite","volume":"11","author":"Forli","year":"2016","journal-title":"Nat. Protoc."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib22","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1529\/biophysj.106.082313","article-title":"On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins","volume":"91","author":"Forrest","year":"2006","journal-title":"Biophys. J."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib23","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1146\/annurev.micro.51.1.97","article-title":"Hemoglobin metabolism in the malaria parasite Plasmodium falciparum","volume":"51","author":"Francis","year":"1997","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib24","doi-asserted-by":"crossref","first-page":"3185","DOI":"10.1093\/bioinformatics\/btp562","article-title":"EasyMIFs and SiteHound: A toolkit for the identification of ligand-binding sites in protein structures","volume":"25","author":"Ghersi","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib25","doi-asserted-by":"crossref","first-page":"D1045","DOI":"10.1093\/nar\/gkv1072","article-title":"BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology","volume":"44","author":"Gilson","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib70","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1093\/bioinformatics\/btl655","article-title":"Biskit--a software platform for structural bioinformatics","volume":"23","author":"Gr\u00fcnberg","year":"2007","journal-title":"Bioinforma. Oxf. Engl."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib78","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1107\/S2052520616003954","article-title":"The Cambridge Structural Database","volume":"72","author":"Groom","year":"2016","journal-title":"Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib26","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S0049-3848(00)00399-6","article-title":"The direct thrombin inhibitor melagatran and its oral prodrug H 376\/95: Intestinal absorption properties, biochemical and pharmacodynamic effects","volume":"101","author":"Gustafsson","year":"2001","journal-title":"Thromb. Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib27","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/prot.10115","article-title":"Principles of docking: An overview of search algorithms and a guide to scoring functions","volume":"47","author":"Halperin","year":"2002","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib28","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/S0959-440X(02)00308-1","article-title":"Molecular dynamics simulations","volume":"12","author":"Hansson","year":"2002","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib29","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.2174\/092986711795029573","article-title":"Bio-inspired algorithms applied to molecular docking simulations","volume":"18","author":"Heberl\u00e9","year":"2011","journal-title":"Curr. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib30","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/S1093-3263(98)00002-3","article-title":"LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins","volume":"15","author":"Hendlich","year":"1997","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib31","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/jmr.984","article-title":"Computational approaches to identifying and characterizing protein binding sites for ligand design","volume":"23","author":"Henrich","year":"2010","journal-title":"J. Mol. Recognit. JMR"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib32","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1089\/omi.2009.0045","article-title":"MetaPocket: A meta approach to improve protein ligand binding site prediction","volume":"13","author":"Huang","year":"2009","journal-title":"OMICS J. Integr. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib79","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1021\/ci010056s","article-title":"Enhanced CACTVS Browser of the Open NCI Database","volume":"42","author":"Ihlenfeldt","year":"2002","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib33","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1472-6807-6-19","article-title":"LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation","volume":"6","author":"Huang","year":"2006","journal-title":"BMC Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib34","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1021\/ci3001277","article-title":"ZINC: A free tool to discover chemistry for biology","volume":"52","author":"Irwin","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib76","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-15-S16-S7","article-title":"Bhageerath-H: A homology\/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins","volume":"15","author":"Jayaram","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib71","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"K\u00e4llberg","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib35","doi-asserted-by":"crossref","first-page":"3979","DOI":"10.1021\/jm9704098","article-title":"Viracept (nelfinavir mesylate, AG1343): A potent, orally bioavailable inhibitor of HIV-1 protease","volume":"40","author":"Kaldor","year":"1997","journal-title":"J. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib36","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/prot.20149","article-title":"Comparative evaluation of eight docking tools for docking and virtual screening accuracy","volume":"57","author":"Kellenberger","year":"2004","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib72","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib37","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkn750","article-title":"The SWISS-MODEL repository and associated resources","volume":"37","author":"Kiefer","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib74","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib38","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","article-title":"PubChem substance and compound databases","volume":"44","author":"Kim","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib85","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1021\/ci800298z","article-title":"Empirical scoring functions for advanced protein-ligand docking with PLANTS","volume":"49","author":"Korb","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib91","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1002\/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8","article-title":"Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking","volume":"37","author":"Kramer","year":"1999","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib39","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.bpj.2009.11.011","article-title":"Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors","volume":"98","author":"Kuzmanic","year":"2010","journal-title":"Biophys. J."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib73","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1093\/bioinformatics\/18.9.1250","article-title":"ESyPred3D: Prediction of proteins 3D structures","volume":"18","author":"Lambert","year":"2002","journal-title":"Bioinforma. Oxf. Engl."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib40","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.bpc.2010.01.011","article-title":"Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco\/endoplasmic reticulum calcium ATPase","volume":"150","author":"Lape","year":"2010","journal-title":"Biophys. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib41","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","article-title":"Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites","volume":"21","author":"Laurie","year":"2005","journal-title":"Bioinformatics Oxford"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib42","doi-asserted-by":"crossref","first-page":"D1091","DOI":"10.1093\/nar\/gkt1068","article-title":"DrugBank 4.0: Shedding new light on drug metabolism","volume":"42","author":"Law","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib43","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-10-168","article-title":"Fpocket: An open source platform for ligand pocket detection","volume":"10","author":"Le Guilloux","year":"2009","journal-title":"BMC Bioinform."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib44","doi-asserted-by":"crossref","first-page":"6157","DOI":"10.1021\/bi2004558","article-title":"Efficient incorporation of protein flexibility and dynamics into molecular docking simulations","volume":"50","author":"Lill","year":"2011","journal-title":"Biochemistry (Moscow)"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib45","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/S1056-8719(00)00107-6","article-title":"Drug-like properties and the causes of poor solubility and poor permeability","volume":"44","author":"Lipinski","year":"2000","journal-title":"J. Pharmacol. Toxicol. Methods"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib46","unstructured":"Locating Binding Sites in Protein Structures, 2017. (WWW Document). Available at: https:\/\/www.chemcomp.com\/journal\/sitefind.htm (accessed 09.09.17)."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib47","doi-asserted-by":"crossref","first-page":"475","DOI":"10.2174\/138620711795767866","article-title":"Integrating virtual screening and combinatorial chemistry for accelerated drug discovery","volume":"14","author":"L\u00f3pez-Vallejo","year":"2011","journal-title":"Comb. Chem. High Throughput Screen."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib48","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1002\/cmdc.200700270","article-title":"Computer-aided design and synthesis of nonpeptidic plasmepsin II and IV inhibitors","volume":"3","author":"Luksch","year":"2008","journal-title":"Chem. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib49","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/nrd3368","article-title":"Impact of high-throughput screening in biomedical research","volume":"10","author":"Macarron","year":"2011","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib50","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","article-title":"Comparative protein structure modeling of genes and genomes","volume":"29","author":"Mart\u00ed-Renom","year":"2000","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib86","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1021\/ci100436p","article-title":"FRED Pose Prediction and Virtual Screening Accuracy","volume":"51","author":"McGann","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib51","doi-asserted-by":"crossref","first-page":"146","DOI":"10.2174\/157340911795677602","article-title":"Molecular docking: A powerful approach for structure-based drug discovery","volume":"7","author":"Meng","year":"2011","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib52","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/S0140-6736(12)60034-8","article-title":"Global malaria mortality between 1980 and 2010: A systematic analysis","volume":"379","author":"Murray","year":"2012","journal-title":"Lancet London"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib88","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1007\/s10822-012-9547-0","article-title":"Docking and scoring with ICM: The benchmarking results and strategies for improvement","volume":"26","author":"Neves","year":"2012","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib53","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.jbiotec.2011.12.005","article-title":"Structure-based computational analysis of protein binding sites for function and druggability prediction","volume":"159","author":"Nisius","year":"2012","journal-title":"J. Biotechnol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib54","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An open chemical toolbox","volume":"3","author":"O\u2019Boyle","year":"2011","journal-title":"J. Cheminform."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib55","doi-asserted-by":"crossref","first-page":"nrd2275","DOI":"10.1038\/nrd2275","article-title":"Target validation: Determining druggability","volume":"6","author":"Owens","year":"2007","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib56","doi-asserted-by":"crossref","first-page":"351","DOI":"10.4103\/0976-500X.103704","article-title":"Protein data bank","volume":"3","author":"Parasuraman","year":"2012","journal-title":"J. Pharmacol. Pharmacother."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib57","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera \u2013 A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib58","doi-asserted-by":"crossref","first-page":"D465","DOI":"10.1093\/nar\/gkq1091","article-title":"ModBase, a database of annotated comparative protein structure models, and associated resources","volume":"39","author":"Pieper","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib59","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1016\/S0022-3565(24)35162-6","article-title":"Inhibition of epidermal growth factor receptor-associated tyrosine phosphorylation in human carcinomas with CP-358,774: Dynamics of receptor inhibition in situ and antitumor effects in athymic mice","volume":"291","author":"Pollack","year":"1999","journal-title":"J. Pharmacol. Exp. Ther."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib89","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0812s18","article-title":"Flexible ligand docking with Glide","author":"Repasky","year":"2007","journal-title":"Curr. Protoc. Bioinforma"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib75","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: A unified platform for automated protein structure and function prediction","volume":"5","author":"Roy","year":"2010","journal-title":"Nat. Protoc."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib84","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003571","article-title":"rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids","volume":"10","author":"Ruiz-Carmona","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib60","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1126\/science.289.5486.1938","article-title":"Structural mechanism for STI-571 inhibition of abelson tyrosine kinase","volume":"289","author":"Schindler","year":"2000","journal-title":"Science"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib82","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gki481","article-title":"PatchDock and SymmDock: Servers for rigid and symmetric docking","volume":"33","author":"Schneidman-Duhovny","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib61","doi-asserted-by":"crossref","first-page":"259","DOI":"10.2174\/1386207043328706","article-title":"Virtual screening methods that complement HTS","volume":"7","author":"Stahura","year":"2004","journal-title":"Comb. Chem. High Throughput Screen."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib62","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1021\/ci800420z","article-title":"Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results","volume":"49","author":"ten Brink","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib63","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.2174\/1381612033454595","article-title":"Conformational flexibility models for the receptor in structure based drug design","volume":"9","author":"Teodoro","year":"2003","journal-title":"Curr. Pharm. Des."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib64","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib65","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/(SICI)1098-2299(199903\/04)46:3\/4<176::AID-DDR4>3.0.CO;2-6","article-title":"Development of neuraminidase inhibitors as anti-influenza virus drugs","volume":"46","author":"Varghese","year":"1999","journal-title":"Drug Dev. Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib90","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/prot.10465","article-title":"Improved protein-ligand docking using GOLD","volume":"52","author":"Verdonk","year":"2003","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib66","doi-asserted-by":"crossref","first-page":"901","DOI":"10.2174\/1568026615666150825142002","article-title":"Advances in computational structure-based drug design and application in drug discovery","volume":"16","author":"Wang","year":"2016","journal-title":"Curr. Top. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib67","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1752-153X-1-7","article-title":"PocketPicker: Analysis of ligand binding-sites with shape descriptors","volume":"1","author":"Weisel","year":"2007","journal-title":"Chem. Cent. J."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib77","doi-asserted-by":"crossref","unstructured":"Williams, A.J., 2010. ChemSpider: Integrating Structure-Based Resources Distributed across the Internet, in: Enhancing Learning with Online Resources, Social Networking, and Digital Libraries, ACS Symposium Series. American Chemical Society, pp. 23\u201339. https:\/\/doi.org\/10.1021\/bk-2010-1060.ch002","DOI":"10.1021\/bk-2010-1060.ch002"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib80","doi-asserted-by":"crossref","first-page":"D801","DOI":"10.1093\/nar\/gks1065","article-title":"HMDB 3.0--The Human Metabolome Database in 2013","volume":"41","author":"Wishart","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib68","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/978-1-4939-1465-4_17","article-title":"Methods for predicting protein-ligand binding sites","volume":"1215","author":"Xie","year":"2015","journal-title":"Methods Mol. Biol. Clifton"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib83","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1002\/prot.20035","article-title":"GEMDOCK: A generic evolutionary method for molecular docking","volume":"55","author":"Yang","year":"2004","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20275-6_bib69","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1002\/jmr.2266","article-title":"Latest developments in molecular docking: 2010\u20132011 in review","volume":"26","author":"Yuriev","year":"2013","journal-title":"J. Mol. Recognit. JMR"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202756?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202756?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T21:07:59Z","timestamp":1751576879000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338202756"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":91,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20275-6","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}