{"id":"https://openalex.org/W2461903645","doi":"https://doi.org/10.1021/acs.jcim.6b00248","title":"Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives","display_name":"Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives","publication_year":2016,"publication_date":"2016-07-06","ids":{"openalex":"https://openalex.org/W2461903645","doi":"https://doi.org/10.1021/acs.jcim.6b00248","mag":"2461903645","pmid":"https://pubmed.ncbi.nlm.nih.gov/27384036"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00248","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00248","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/A5004299489","display_name":"Richard K. Belew","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard K. Belew","raw_affiliation_strings":["Cognitive\rScience, University of California San Diego, La Jolla, California 92093, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cognitive\rScience, University of California San Diego, La Jolla, California 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068867875","display_name":"Stefano Forli","orcid":"https://orcid.org/0000-0002-5964-7111"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefano Forli","raw_affiliation_strings":["Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040337866","display_name":"David S. Goodsell","orcid":"https://orcid.org/0000-0002-5932-2130"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David S. Goodsell","raw_affiliation_strings":["Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032027072","display_name":"TJ O'Donnell","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. J. O\u2019Donnell","raw_affiliation_strings":["gNova, San Diego, California 92104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"gNova, San Diego, California 92104, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058956938","display_name":"Arthur J. Olson","orcid":"https://orcid.org/0000-0003-0558-4618"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arthur J. Olson","raw_affiliation_strings":["Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Integrative\rStructural and Computational Biology, The Scripps Research Institute, La\rJolla, California 92037, United States","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5004299489"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":1.4415,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.83669153,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"56","issue":"8","first_page":"1597","last_page":"1607"},"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/T11440","display_name":"Click Chemistry and Applications","score":0.9710000157356262,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9639999866485596,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.8338623046875},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5557945370674133},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5495820641517639},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38986796140670776},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.36880189180374146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32112187147140503},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21204155683517456},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.18429780006408691},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1672680675983429},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.12496283650398254}],"concepts":[{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.8338623046875},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5557945370674133},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5495820641517639},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38986796140670776},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.36880189180374146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32112187147140503},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21204155683517456},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.18429780006408691},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1672680675983429},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.12496283650398254}],"mesh":[{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.6b00248","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00248","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:27384036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27384036","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:4458222","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5023760","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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6700000166893005}],"awards":[{"id":"https://openalex.org/G345001416","display_name":null,"funder_award_id":"P50 GM103368","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6155115457","display_name":null,"funder_award_id":"P50GM103368","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1991286793","https://openalex.org/W2001988771","https://openalex.org/W2002063821","https://openalex.org/W2030121478","https://openalex.org/W2041877730","https://openalex.org/W2044444984","https://openalex.org/W2083385715","https://openalex.org/W2102384571","https://openalex.org/W2102839822","https://openalex.org/W2105668062","https://openalex.org/W2106393550","https://openalex.org/W2114326383","https://openalex.org/W2133990480","https://openalex.org/W2134967712","https://openalex.org/W2161085303","https://openalex.org/W2169678694","https://openalex.org/W2177551934","https://openalex.org/W2293744162","https://openalex.org/W2320534770","https://openalex.org/W2336040088","https://openalex.org/W2485749800"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"We":[0],"describe":[1],"ADChemCast,":[2],"a":[3,13,17,55],"method":[4,112],"for":[5,77,113],"using":[6],"results":[7],"from":[8,72,99],"virtual":[9],"screening":[10],"to":[11,25,69,89],"create":[12],"richer":[14],"representation":[15],"of":[16,28,34,41,57,60,81,93,102,110],"target":[18],"binding":[19,116],"site,":[20],"which":[21],"may":[22],"be":[23],"used":[24,68],"improve":[26,90],"ranking":[27,92],"compounds":[29,94],"and":[30,62,106],"characterize":[31],"the":[32,73,91,100,108,111],"determinants":[33],"ligand-receptor":[35],"specificity.":[36],"ADChemCast":[37,88],"clusters":[38],"docked":[39],"conformations":[40],"ligands":[42],"based":[43],"on":[44],"shared":[45],"pairwise":[46],"receptor-ligand":[47],"interactions":[48],"within":[49],"chemically":[50],"similar":[51],"structural":[52],"fragments,":[53],"building":[54],"set":[56],"attributes":[58,76,117],"characteristic":[59],"binders":[61],"nonbinders.":[63],"Machine":[64],"learning":[65],"is":[66],"then":[67],"build":[70],"rules":[71],"most":[74],"informational":[75],"use":[78,87],"in":[79,95,118],"reranking":[80],"compounds.":[82],"In":[83],"this":[84],"report,":[85],"we":[86],"11":[96],"diverse":[97],"proteins":[98],"Database":[101],"Useful":[103],"Decoys-Enhanced":[104],"(DUD-E)":[105],"demonstrate":[107],"utility":[109],"characterizing":[114],"relevant":[115],"HIV":[119],"reverse":[120],"transcriptase.":[121]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}