{"id":"https://openalex.org/W2025970767","doi":"https://doi.org/10.1021/ci2002507","title":"Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening","display_name":"Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening","publication_year":2011,"publication_date":"2011-10-23","ids":{"openalex":"https://openalex.org/W2025970767","doi":"https://doi.org/10.1021/ci2002507","mag":"2025970767","pmid":"https://pubmed.ncbi.nlm.nih.gov/22017385"},"language":"en","primary_location":{"id":"doi:10.1021/ci2002507","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2002507","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3264743","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074840579","display_name":"Jui-Hua Hsieh","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jui-Hua Hsieh","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085993088","display_name":"Shuangye Yin","orcid":"https://orcid.org/0000-0002-2779-2584"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuangye Yin","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087601019","display_name":"Xiang S. Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiang S. Wang","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062471687","display_name":"Shubin Liu","orcid":"https://orcid.org/0000-0001-9331-0427"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shubin Liu","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033490428","display_name":"Nikolay V. Dokholyan","orcid":"https://orcid.org/0000-0002-8225-4025"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I2801345345","display_name":"Cancer Institute (WIA)","ror":"https://ror.org/01tc10z29","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I2801345345"]}],"countries":["IN","US"],"is_corresponding":true,"raw_author_name":"Nikolay V. Dokholyan","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","Penn State Cancer Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Penn State Cancer Institute","institution_ids":["https://openalex.org/I2801345345","https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078536199","display_name":"Alexander Tropsha","orcid":"https://orcid.org/0000-0003-3802-8896"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander Tropsha","raw_affiliation_strings":["Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, Eshelman School of Pharmacy, \u2021Department of Biochemistry and Biophysics, and \u00a7Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5033490428","https://openalex.org/A5078536199"],"corresponding_institution_ids":["https://openalex.org/I114027177","https://openalex.org/I130769515","https://openalex.org/I2801345345"],"apc_list":null,"apc_paid":null,"fwci":4.2404,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.9431814,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"52","issue":"1","first_page":"16","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9973000288009644,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9526000022888184,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.8755697011947632},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.8058754801750183},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6027520895004272},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5626320838928223},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5154951214790344},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4134008288383484},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3859696090221405},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.22203391790390015},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17156562209129333},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16992419958114624},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.15951010584831238}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.8755697011947632},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8058754801750183},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6027520895004272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5626320838928223},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5154951214790344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4134008288383484},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3859696090221405},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.22203391790390015},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17156562209129333},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16992419958114624},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.15951010584831238},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011480","descriptor_name":"Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011480","descriptor_name":"Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011480","descriptor_name":"Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011480","descriptor_name":"Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci2002507","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2002507","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:22017385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22017385","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:pubmedcentral.nih.gov:3264743","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3264743","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:3264743","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3264743","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.5299999713897705},{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.4300000071525574}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332600","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33"},{"id":"https://openalex.org/F4320337701","display_name":"North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W83502394","https://openalex.org/W1596929908","https://openalex.org/W1605578858","https://openalex.org/W1963723282","https://openalex.org/W1968302589","https://openalex.org/W1970208561","https://openalex.org/W1972148009","https://openalex.org/W1985300726","https://openalex.org/W1986240377","https://openalex.org/W1993403967","https://openalex.org/W1996966884","https://openalex.org/W2000825058","https://openalex.org/W2001816314","https://openalex.org/W2003356525","https://openalex.org/W2012084558","https://openalex.org/W2015907087","https://openalex.org/W2025135899","https://openalex.org/W2030121478","https://openalex.org/W2048172038","https://openalex.org/W2049046803","https://openalex.org/W2051261289","https://openalex.org/W2058220696","https://openalex.org/W2058433776","https://openalex.org/W2058820833","https://openalex.org/W2059317968","https://openalex.org/W2067455153","https://openalex.org/W2068672372","https://openalex.org/W2071932467","https://openalex.org/W2079398727","https://openalex.org/W2081322171","https://openalex.org/W2085564033","https://openalex.org/W2087661061","https://openalex.org/W2088423689","https://openalex.org/W2090035064","https://openalex.org/W2092501219","https://openalex.org/W2101958915","https://openalex.org/W2108257090","https://openalex.org/W2121895929","https://openalex.org/W2123969193","https://openalex.org/W2127760066","https://openalex.org/W2128245586","https://openalex.org/W2128332459","https://openalex.org/W2128991310","https://openalex.org/W2143422060","https://openalex.org/W2144482528","https://openalex.org/W2153635508","https://openalex.org/W2154714625","https://openalex.org/W2160821308","https://openalex.org/W2169562071","https://openalex.org/W3081595573","https://openalex.org/W4231649355"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W1570419641","https://openalex.org/W4386509167","https://openalex.org/W4362464865","https://openalex.org/W2098840560","https://openalex.org/W4302604134","https://openalex.org/W2768880727","https://openalex.org/W2113146994","https://openalex.org/W2073081213","https://openalex.org/W2621548818"],"abstract_inverted_index":{"Poor":[0],"performance":[1,70],"of":[2,44,71,75,78,87,102,114,133,141,150,153,177,184,189,307,314],"scoring":[3,21,126,160,166],"functions":[4],"is":[5,15],"a":[6,41,92,122,246,304],"well-known":[7],"bottleneck":[8],"in":[9,19,73,119,136,174,230],"structure-based":[10,165,315],"virtual":[11],"screening":[12,191],"(VS),":[13],"which":[14],"most":[16],"frequently":[17],"manifested":[18],"the":[20,69,85,112,142,147,151,190,212,220,254,257,265,312],"functions'":[22],"inability":[23],"to":[24,40,95,130,207,275,303,310],"discriminate":[25],"between":[26],"true":[27,79],"ligands":[28,222,267],"vs":[29],"known":[30],"nonbinders":[31],"(therefore":[32],"designated":[33],"as":[34,62],"binding":[35],"decoys).":[36],"This":[37,157],"deficiency":[38],"leads":[39,129],"large":[42],"number":[43],"false":[45],"positive":[46],"hits":[47],"resulting":[48],"from":[49,84,99,146],"VS.":[50],"We":[51,109,193,217,239,287],"have":[52,90,208],"hypothesized":[53],"that":[54,111,203,219,250,264,289],"filtering":[55],"out":[56,176],"or":[57],"penalizing":[58],"docking":[59,107],"poses":[60,103],"recognized":[61],"non-native":[63],"(i.e.,":[64],"pose":[65,97,116],"decoys)":[66],"should":[67],"improve":[68,311],"VS":[72,137,185,201,248,285,292],"terms":[74],"improved":[76],"identification":[77],"binders.":[80],"Using":[81],"several":[82,163,199],"concepts":[83],"field":[86],"cheminformatics,":[88],"we":[89,262],"developed":[91],"novel":[93,200],"approach":[94,293],"identifying":[96],"decoys":[98,188],"an":[100],"ensemble":[101],"generated":[104],"by":[105],"computational":[106],"procedures.":[108],"demonstrate":[110],"use":[113],"target-specific":[115],"(scoring)":[117],"filter":[118],"combination":[120],"with":[121,198,232,244],"physical":[123],"force":[124],"field-based":[125],"function":[127,161],"(MedusaScore)":[128],"significant":[131],"improvement":[132],"hit":[134],"rates":[135],"studies":[138],"for":[139,283],"12":[140],"13":[143,178],"benchmark":[144],"sets":[145,180],"clustered":[148],"version":[149],"Database":[152],"Useful":[154],"Decoys":[155],"(DUD).":[156],"new":[158],"hybrid":[159,196],"outperforms":[162],"conventional":[164],"functions,":[167],"including":[168],"XSCORE::HMSCORE,":[169],"ChemScore,":[170],"PLP,":[171],"and":[172,237,256,296],"Chemgauss3,":[173],"6":[175],"data":[179,215],"at":[181],"early":[182],"stage":[183],"(up":[186],"1%":[187],"database).":[192],"compare":[194,241],"our":[195,224,242,270],"method":[197,225,243,249,271],"methods":[202,235],"were":[204],"recently":[205],"reported":[206],"good":[209],"performances":[210],"on":[211],"same":[213],"DUD":[214],"sets.":[216],"find":[218,263],"retrieved":[221,268,277],"using":[223,269,278],"are":[226,272],"chemically":[227],"more":[228],"diverse":[229],"comparison":[231],"two":[233],"ligand-based":[234],"(FieldScreen":[236],"FLAP::LBX).":[238],"also":[240,251],"FLAP::RBLB,":[245,279],"high-performance":[247],"utilizes":[252],"both":[253],"receptor":[255],"cognate":[258],"ligand":[259],"structures.":[260],"Interestingly,":[261],"top":[266],"highly":[273],"complementary":[274],"those":[276],"hinting":[280],"effective":[281],"directions":[282],"best":[284],"applications.":[286],"suggest":[288],"this":[290],"integrative":[291],"combining":[294],"cheminformatics":[295],"molecular":[297],"mechanics":[298],"methodologies":[299],"may":[300],"be":[301],"applied":[302],"broad":[305],"variety":[306],"protein":[308],"targets":[309],"outcome":[313],"drug":[316],"discovery":[317],"studies.":[318]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}