{"id":"https://openalex.org/W2912315505","doi":"https://doi.org/10.1007/s10822-019-00185-0","title":"Predicting protein\u2013ligand binding modes for CELPP and GC3: workflows and insight","display_name":"Predicting protein\u2013ligand binding modes for CELPP and GC3: workflows and insight","publication_year":2019,"publication_date":"2019-01-28","ids":{"openalex":"https://openalex.org/W2912315505","doi":"https://doi.org/10.1007/s10822-019-00185-0","mag":"2912315505","pmid":"https://pubmed.ncbi.nlm.nih.gov/30689079"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-019-00185-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-019-00185-0","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":true,"raw_author_name":"Xianjin Xu","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","Informatics Institute, University of Missouri, 65211, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101650425","display_name":"Zhiwei Ma","orcid":"https://orcid.org/0000-0001-9243-2211"},"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":"Zhiwei Ma","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","Informatics Institute, University of Missouri, 65211, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103252924","display_name":"Rui Duan","orcid":"https://orcid.org/0000-0003-1646-4013"},"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":"Rui Duan","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","Informatics Institute, University of Missouri, 65211, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, 65211, Columbia, MO, 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":false,"raw_author_name":"Xiaoqin Zou","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","Informatics Institute, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA"],"raw_orcid":"https://orcid.org/0000-0003-0637-8648","affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, 65211, Columbia, MO, USA. zoux@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032107354"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.9402,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73842414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"3","first_page":"367","last_page":"374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994000196456909,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9990000128746033,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5520287156105042},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5279996395111084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5195153951644897},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.44974285364151},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4112311601638794},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32117611169815063},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15995556116104126},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1415419578552246},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.10481759905815125},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.07884949445724487}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5520287156105042},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5279996395111084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5195153951644897},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.44974285364151},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4112311601638794},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32117611169815063},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15995556116104126},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1415419578552246},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.10481759905815125},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.07884949445724487}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-019-00185-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-019-00185-0","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:30689079","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30689079","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:5991982","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6494980","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/G1765163128","display_name":null,"funder_award_id":"CNS-1429294","funder_id":"https://openalex.org/F4320337388","funder_display_name":"Division of Computer and Network Systems"},{"id":"https://openalex.org/G2699039349","display_name":null,"funder_award_id":"R01HL142301","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"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"},{"id":"https://openalex.org/G6779582418","display_name":null,"funder_award_id":"R01HL126774","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309568","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1986240377","https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2000864931","https://openalex.org/W2028609644","https://openalex.org/W2038542598","https://openalex.org/W2044098211","https://openalex.org/W2055043387","https://openalex.org/W2067732724","https://openalex.org/W2070880994","https://openalex.org/W2072180710","https://openalex.org/W2077417417","https://openalex.org/W2078374001","https://openalex.org/W2090431249","https://openalex.org/W2105527266","https://openalex.org/W2117897510","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2142678478","https://openalex.org/W2145682943","https://openalex.org/W2151736966","https://openalex.org/W2169176218","https://openalex.org/W2169562071","https://openalex.org/W2337273834","https://openalex.org/W2346710580","https://openalex.org/W2364255377","https://openalex.org/W2527541313","https://openalex.org/W2727656886","https://openalex.org/W2767222721","https://openalex.org/W2774738748","https://openalex.org/W2793534579","https://openalex.org/W2979731220"],"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":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-03T08:25:01.440150","created_date":"2025-10-10T00:00:00"}
