{"id":"https://openalex.org/W2762631622","doi":"https://doi.org/10.1093/bioinformatics/btx638","title":"Machine learning accelerates MD-based binding pose prediction between ligands and proteins","display_name":"Machine learning accelerates MD-based binding pose prediction between ligands and proteins","publication_year":2017,"publication_date":"2017-10-10","ids":{"openalex":"https://openalex.org/W2762631622","doi":"https://doi.org/10.1093/bioinformatics/btx638","mag":"2762631622","pmid":"https://pubmed.ncbi.nlm.nih.gov/29040432"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/770/25117719/btx638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/770/25117719/btx638.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072608872","display_name":"Kei Terayama","orcid":"https://orcid.org/0000-0003-3914-248X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kei Terayama","raw_affiliation_strings":["Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan"],"raw_orcid":"https://orcid.org/0000-0003-3914-248X","affiliations":[{"raw_affiliation_string":"Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043360512","display_name":"Hiroaki Iwata","orcid":"https://orcid.org/0000-0001-9791-0008"},"institutions":[{"id":"https://openalex.org/I4210167395","display_name":"Foundation for Biomedical Research and Innovation","ror":"https://ror.org/05xe40a72","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210167395"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Iwata","raw_affiliation_strings":["Foundation for Biomedical Research and Innovation, Hyogo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Foundation for Biomedical Research and Innovation, Hyogo, Japan","institution_ids":["https://openalex.org/I4210167395"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023816779","display_name":"Mitsugu Araki","orcid":"https://orcid.org/0000-0002-7810-4905"},"institutions":[{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mitsugu Araki","raw_affiliation_strings":["RIKEN Advanced Institute for Computational Science, Hyogo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Advanced Institute for Computational Science, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046211758","display_name":"Yasushi Okuno","orcid":"https://orcid.org/0000-0003-3596-4208"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasushi Okuno","raw_affiliation_strings":["Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan","RIKEN Advanced Institute for Computational Science, Hyogo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"RIKEN Advanced Institute for Computational Science, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070597006","display_name":"Koji Tsuda","orcid":"https://orcid.org/0000-0002-4288-1606"},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Koji Tsuda","raw_affiliation_strings":["Center for Materials Research by Information Integration, NIMS, Ibaraki, Japan","Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan","RIKEN Center for Advanced Intelligence Project, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Materials Research by Information Integration, NIMS, Ibaraki, Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"RIKEN Center for Advanced Intelligence Project, Tokyo, Japan","institution_ids":["https://openalex.org/I4210126580"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070597006","https://openalex.org/A5072608872"],"corresponding_institution_ids":["https://openalex.org/I4210126580","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6307,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.9122018,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"34","issue":"5","first_page":"770","last_page":"778"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9294999837875366,"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":0.9294999837875366,"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":0.04619999974966049,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.004100000020116568,"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/computer-science","display_name":"Computer science","score":0.7313453555107117},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5459585785865784},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4892556667327881},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47993236780166626},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.43667107820510864},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4121546447277069},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4117644429206848},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3925078511238098},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3653905689716339},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2163701355457306},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16552528738975525},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11190643906593323}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7313453555107117},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5459585785865784},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4892556667327881},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47993236780166626},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.43667107820510864},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4121546447277069},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4117644429206848},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3925078511238098},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3653905689716339},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2163701355457306},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16552528738975525},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11190643906593323},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":true},{"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/770/25117719/btx638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29040432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29040432","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:irdb.nii.ac.jp:01221:0000188643","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/233911","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal article"},{"id":"pmh:oai:europepmc.org:4991229","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6030886","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":{"id":"doi:10.1093/bioinformatics/btx638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/770/25117719/btx638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1053371971","display_name":null,"funder_award_id":"JPMJCR1311","funder_id":"https://openalex.org/F4320320907","funder_display_name":"Japan Science and Technology Corporation"},{"id":"https://openalex.org/G2899114271","display_name":null,"funder_award_id":"JPMJCR1502","funder_id":"https://openalex.org/F4320320907","funder_display_name":"Japan Science and Technology Corporation"}],"funders":[{"id":"https://openalex.org/F4320309809","display_name":"Cell Science Research Foundation","ror":"https://ror.org/01v3bqg10"},{"id":"https://openalex.org/F4320320907","display_name":"Japan Science and Technology Corporation","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320323316","display_name":"Shionogi","ror":"https://ror.org/01v3bqg10"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W8700100","https://openalex.org/W1573009101","https://openalex.org/W1714211023","https://openalex.org/W1881419322","https://openalex.org/W1911551976","https://openalex.org/W1916369423","https://openalex.org/W1966078827","https://openalex.org/W1967348240","https://openalex.org/W1968984443","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1978330227","https://openalex.org/W1980989103","https://openalex.org/W1988076192","https://openalex.org/W1993403967","https://openalex.org/W1998498767","https://openalex.org/W2019574809","https://openalex.org/W2030980866","https://openalex.org/W2031390939","https://openalex.org/W2033882981","https://openalex.org/W2039353947","https://openalex.org/W2044172327","https://openalex.org/W2046029732","https://openalex.org/W2059013803","https://openalex.org/W2067174909","https://openalex.org/W2103631613","https://openalex.org/W2112420033","https://openalex.org/W2112855704","https://openalex.org/W2114320488","https://openalex.org/W2115251824","https://openalex.org/W2130479394","https://openalex.org/W2139880162","https://openalex.org/W2142868265","https://openalex.org/W2147993766","https://openalex.org/W2148893085","https://openalex.org/W2161605421","https://openalex.org/W2166765429","https://openalex.org/W2168405694","https://openalex.org/W2192203593","https://openalex.org/W2257979135","https://openalex.org/W3125733173"],"related_works":["https://openalex.org/W4312103688","https://openalex.org/W2575434942","https://openalex.org/W2480711475","https://openalex.org/W2047838177","https://openalex.org/W2329052364","https://openalex.org/W2064383522","https://openalex.org/W2023156907","https://openalex.org/W3113347309","https://openalex.org/W4282913408","https://openalex.org/W4308805210"],"abstract_inverted_index":{"Motivation:":[0],"Fast":[1],"and":[2,15,44,138,174,177],"accurate":[3,16,30],"prediction":[4,32],"of":[5,18,22,78,110,130,162],"protein-ligand":[6,79],"binding":[7,19,80,115,124],"structures":[8,55],"is":[9],"indispensable":[10],"for":[11,113,158],"structure-based":[12],"drug":[13,23,27],"design":[14],"estimation":[17],"free":[20],"energy":[21],"candidate":[24],"molecules":[25],"in":[26],"discovery.":[28],"Recently,":[29],"pose":[31,125],"methods":[33],"based":[34],"on":[35,61,181],"short":[36],"Molecular":[37],"Dynamics":[38],"(MD)":[39],"simulations,":[40],"such":[41],"as":[42],"MM-PBSA":[43],"MM-GBSA,":[45],"among":[46],"generated":[47],"docking":[48],"poses":[49,81],"have":[50],"been":[51],"used.":[52],"Since":[53],"molecular":[54,163],"obtained":[56],"from":[57],"MD":[58,111],"simulation":[59],"depend":[60],"the":[62,66,108,143],"initial":[63,70,90],"condition,":[64],"taking":[65],"average":[67],"over":[68],"different":[69,89],"conditions":[71],"leads":[72],"to":[73,120,165],"better":[74],"accuracy.":[75,152],"Prediction":[76],"accuracy":[77],"can":[82,105,146,155],"be":[83,147,156],"improved":[84],"with":[85,126],"multiple":[86],"runs":[87,112],"at":[88,183,195],"velocity.":[91],"Results:":[92],"This":[93,153],"paper":[94],"shows":[95],"that":[96,142],"a":[97,122,127],"machine":[98],"learning":[99],"method,":[100],"called":[101],"Best":[102],"Arm":[103],"Identification,":[104],"optimally":[106],"control":[107],"number":[109,129],"each":[114],"pose.":[116],"It":[117],"allows":[118],"us":[119],"identify":[121],"correct":[123],"minimum":[128],"total":[131],"runs.":[132],"Our":[133],"experiment":[134],"using":[135],"three":[136],"proteins":[137],"eight":[139],"inhibitors":[140],"showed":[141],"computational":[144,171],"cost":[145],"reduced":[148],"substantially":[149],"without":[150],"sacrificing":[151],"method":[154],"applied":[157],"controlling":[159],"all":[160],"kinds":[161],"simulations":[164],"obtain":[166],"best":[167],"results":[168],"under":[169],"restricted":[170],"resources.":[172],"Availability":[173],"implementation:":[175],"Code":[176],"data":[178,192],"are":[179,193],"available":[180,194],"GitHub":[182],"https://github.com/tsudalab/bpbi.":[184],"Contact:":[185],"terayama@cbms.k.u-tokyo.ac.jp":[186],"or":[187],"tsuda@k.u-tokyo.ac.jp.":[188],"Supplementary":[189,191],"information:":[190],"Bioinformatics":[196],"online.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":2}],"updated_date":"2026-05-28T09:10:13.091523","created_date":"2025-10-10T00:00:00"}
