{"id":"https://openalex.org/W2727656886","doi":"https://doi.org/10.1007/s10822-017-0038-1","title":"Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015","display_name":"Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015","publication_year":2017,"publication_date":"2017-07-01","ids":{"openalex":"https://openalex.org/W2727656886","doi":"https://doi.org/10.1007/s10822-017-0038-1","mag":"2727656886","pmid":"https://pubmed.ncbi.nlm.nih.gov/28668990"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-017-0038-1","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-017-0038-1","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5032107354","display_name":"Xianjin Xu","orcid":"https://orcid.org/0000-0002-5011-2997"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xianjin Xu","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053084378","display_name":"Chengfei Yan","orcid":"https://orcid.org/0000-0002-2010-6668"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengfei Yan","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA","Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081082371","display_name":"Xiaoqin Zou","orcid":"https://orcid.org/0000-0003-0637-8648"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoqin Zou","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA"],"raw_orcid":"https://orcid.org/0000-0003-0637-8648","affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081082371"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":3690,"currency":"USD","value_usd":3690},"apc_paid":null,"fwci":2.1252,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.88646738,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"8","first_page":"689","last_page":"699"},"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":0.994700014591217,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9769999980926514,"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/docking","display_name":"Docking (animal)","score":0.7982596158981323},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.6752718687057495},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5212631821632385},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.5053148865699768},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4827808439731598},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47199466824531555},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.46375659108161926},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42028868198394775},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.418140172958374},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3271332085132599},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3027932047843933},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2986461818218231},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.26899582147598267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20804202556610107},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13337761163711548},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.12431129813194275}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7982596158981323},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.6752718687057495},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5212631821632385},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.5053148865699768},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4827808439731598},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47199466824531555},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.46375659108161926},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42028868198394775},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.418140172958374},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3271332085132599},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3027932047843933},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2986461818218231},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.26899582147598267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20804202556610107},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13337761163711548},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.12431129813194275},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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":"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":"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":"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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:10.1007/s10822-017-0038-1","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-017-0038-1","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:28668990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28668990","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:europepmc.org:5072817","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5711532","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":[],"awards":[{"id":"https://openalex.org/G2661217566","display_name":null,"funder_award_id":"R01 GM109980","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2705911549","display_name":null,"funder_award_id":"1429294","funder_id":"https://openalex.org/F4320337388","funder_display_name":"Division of Computer and Network Systems"},{"id":"https://openalex.org/G3029037113","display_name":null,"funder_award_id":"13GRNT16990076","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G5237855735","display_name":null,"funder_award_id":"0953839","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G6057762391","display_name":null,"funder_award_id":"R01GM109980","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320309568","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337388","display_name":"Division of Computer and Network Systems","ror":"https://ror.org/02rdzmk74"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1964458698","https://openalex.org/W1986240377","https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2000864931","https://openalex.org/W2005817231","https://openalex.org/W2013996808","https://openalex.org/W2028609644","https://openalex.org/W2038542598","https://openalex.org/W2067732724","https://openalex.org/W2070880994","https://openalex.org/W2072180710","https://openalex.org/W2072757166","https://openalex.org/W2078374001","https://openalex.org/W2081678229","https://openalex.org/W2090431249","https://openalex.org/W2096729078","https://openalex.org/W2105527266","https://openalex.org/W2127290087","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2145682943","https://openalex.org/W2154055114","https://openalex.org/W2169562071","https://openalex.org/W2301625241","https://openalex.org/W2320034101","https://openalex.org/W2337273834","https://openalex.org/W2346710580","https://openalex.org/W2364255377","https://openalex.org/W2527541313"],"related_works":["https://openalex.org/W2078653892","https://openalex.org/W1974422922","https://openalex.org/W585106548","https://openalex.org/W2106810308","https://openalex.org/W1974879154","https://openalex.org/W2058311929","https://openalex.org/W2089879448","https://openalex.org/W3004756300","https://openalex.org/W4309353019","https://openalex.org/W2007054671"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
