{"id":"https://openalex.org/W2094152931","doi":"https://doi.org/10.1021/ci200126v","title":"Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions","display_name":"Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions","publication_year":2011,"publication_date":"2011-06-22","ids":{"openalex":"https://openalex.org/W2094152931","doi":"https://doi.org/10.1021/ci200126v","mag":"2094152931","pmid":"https://pubmed.ncbi.nlm.nih.gov/21696204"},"language":"en","primary_location":{"id":"doi:10.1021/ci200126v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200126v","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077048241","display_name":"Robert D. Malmstrom","orcid":null},"institutions":[{"id":"https://openalex.org/I55302922","display_name":"The University of Texas Medical Branch at Galveston","ror":"https://ror.org/016tfm930","country_code":"US","type":"education","lineage":["https://openalex.org/I55302922"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert D. Malmstrom","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States","institution_ids":["https://openalex.org/I55302922"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017815970","display_name":"Stanley J. Watowich","orcid":"https://orcid.org/0000-0002-1660-1818"},"institutions":[{"id":"https://openalex.org/I55302922","display_name":"The University of Texas Medical Branch at Galveston","ror":"https://ror.org/016tfm930","country_code":"US","type":"education","lineage":["https://openalex.org/I55302922"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stanley J. Watowich","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States","institution_ids":["https://openalex.org/I55302922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077048241"],"corresponding_institution_ids":["https://openalex.org/I55302922"],"apc_list":null,"apc_paid":null,"fwci":2.1969,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.87637436,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"51","issue":"7","first_page":"1648","last_page":"1655"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7948277592658997},{"id":"https://openalex.org/keywords/decoupling","display_name":"Decoupling (probability)","score":0.6963496804237366},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5206146240234375},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4870658218860626},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.44329822063446045},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.41694432497024536},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.4139564633369446},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3252274692058563},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2878473997116089},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2217378318309784},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.18250104784965515},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.1007915735244751},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07463181018829346}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7948277592658997},{"id":"https://openalex.org/C205606062","wikidata":"https://www.wikidata.org/wiki/Q5249645","display_name":"Decoupling (probability)","level":2,"score":0.6963496804237366},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5206146240234375},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4870658218860626},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.44329822063446045},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.41694432497024536},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4139564633369446},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3252274692058563},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2878473997116089},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2217378318309784},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.18250104784965515},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.1007915735244751},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07463181018829346},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C133731056","wikidata":"https://www.wikidata.org/wiki/Q4917288","display_name":"Control engineering","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci200126v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200126v","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:21696204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21696204","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:europepmc.org:2406046","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3145410","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5600000023841858,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W292723068","https://openalex.org/W408236731","https://openalex.org/W1965762256","https://openalex.org/W1975580333","https://openalex.org/W1980253717","https://openalex.org/W1980949045","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1992793331","https://openalex.org/W1994114759","https://openalex.org/W1997619108","https://openalex.org/W2001368885","https://openalex.org/W2004889188","https://openalex.org/W2007218072","https://openalex.org/W2014433873","https://openalex.org/W2015688756","https://openalex.org/W2017829285","https://openalex.org/W2023181285","https://openalex.org/W2027408247","https://openalex.org/W2036579888","https://openalex.org/W2037535298","https://openalex.org/W2037652551","https://openalex.org/W2042980919","https://openalex.org/W2050333027","https://openalex.org/W2050774715","https://openalex.org/W2051551120","https://openalex.org/W2056179306","https://openalex.org/W2059890035","https://openalex.org/W2071717945","https://openalex.org/W2071791280","https://openalex.org/W2072604508","https://openalex.org/W2073714240","https://openalex.org/W2083385781","https://openalex.org/W2087596773","https://openalex.org/W2089001748","https://openalex.org/W2091734240","https://openalex.org/W2095501702","https://openalex.org/W2103300124","https://openalex.org/W2105668062","https://openalex.org/W2107714804","https://openalex.org/W2115774588","https://openalex.org/W2117620409","https://openalex.org/W2121895929","https://openalex.org/W2127290087","https://openalex.org/W2128494768","https://openalex.org/W2131462376","https://openalex.org/W2131794674","https://openalex.org/W2143141179","https://openalex.org/W2147993766","https://openalex.org/W2149302140","https://openalex.org/W2151942123","https://openalex.org/W2162166182","https://openalex.org/W2163538152","https://openalex.org/W2165526004","https://openalex.org/W2167041509","https://openalex.org/W2949504121"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W4313561376","https://openalex.org/W2320211095","https://openalex.org/W2308164565","https://openalex.org/W3103825105","https://openalex.org/W3027880158","https://openalex.org/W2062768126","https://openalex.org/W1617565119","https://openalex.org/W160381218","https://openalex.org/W2017996710"],"abstract_inverted_index":{"Virtual":[0],"screening":[1,44,148],"of":[2,34,61,69,75],"small":[3,52],"molecule":[4,53],"databases":[5,54],"against":[6],"macromolecular":[7],"targets":[8],"was":[9,119],"used":[10,56],"to":[11,57,141],"identify":[12],"binding":[13,35,82,100],"ligands":[14],"and":[15,37,48,85,98,130],"predict":[16],"their":[17],"lowest":[18],"energy":[19,33,117,134],"bound":[20,47,107],"conformation":[21],"(i.e.,":[22],"pose).":[23],"AutoDock4-generated":[24],"poses":[25,108],"were":[26,55],"rescored":[27],"using":[28],"mean-field":[29],"pathway":[30],"decoupling":[31],"free":[32,83,101,116,133],"calculations":[36,41,74],"evaluated":[38],"if":[39],"these":[40],"improved":[42],"virtual":[43,147],"discrimination":[45],"between":[46,96,127],"nonbound":[49],"ligands.":[50],"Two":[51],"evaluate":[58],"the":[59,62,93,105,111],"effectiveness":[60],"rescoring":[63,118,135],"algorithm":[64],"in":[65,125,146],"correctly":[66],"identifying":[67],"binders":[68,129],"L99A":[70],"T4":[71],"lysozyme.":[72],"Self-dock":[73],"a":[76,138],"database":[77],"containing":[78],"compounds":[79],"with":[80],"known":[81,128],"energies":[84,102],"cocrystal":[86],"structures":[87],"largely":[88],"reproduced":[89],"experimental":[90,99,112],"measurements,":[91],"although":[92],"mean":[94],"difference":[95],"calculated":[97],"increased":[103],"as":[104],"predicted":[106],"diverged":[109],"from":[110],"poses.":[113],"In":[114],"addition,":[115],"more":[120],"accurate":[121],"than":[122],"AutoDock4":[123],"scores":[124],"discriminating":[126],"nonbinders,":[131],"suggesting":[132],"could":[136],"be":[137],"useful":[139],"approach":[140],"reduce":[142],"false":[143],"positive":[144],"predictions":[145],"experiments.":[149]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
