{"id":"https://openalex.org/W2127358457","doi":"https://doi.org/10.1186/s13015-015-0034-8","title":"MoDock: A multi-objective strategy improves the accuracy for molecular docking","display_name":"MoDock: A multi-objective strategy improves the accuracy for molecular docking","publication_year":2015,"publication_date":"2015-02-17","ids":{"openalex":"https://openalex.org/W2127358457","doi":"https://doi.org/10.1186/s13015-015-0034-8","mag":"2127358457","pmid":"https://pubmed.ncbi.nlm.nih.gov/25705248"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-015-0034-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0034-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0034-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0034-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009811756","display_name":"Junfeng Gu","orcid":"https://orcid.org/0000-0003-3359-1890"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junfeng Gu","raw_affiliation_strings":["State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103679192","display_name":"Xu Yang","orcid":"https://orcid.org/0000-0001-9963-6225"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xu Yang","raw_affiliation_strings":["State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100779127","display_name":"Ling Kang","orcid":"https://orcid.org/0000-0003-1004-371X"},"institutions":[{"id":"https://openalex.org/I4210131997","display_name":"Dalian Neusoft University of Information","ror":"https://ror.org/0304ty515","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210131997"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Kang","raw_affiliation_strings":["Department of Computer Science and Technology, Dalian Neusoft Institute of Information, Dalian, 116023 China","Dept. of Comput. Sci. & Technol., Dalian Neusoft Inst. of Inf., Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Dalian Neusoft Institute of Information, Dalian, 116023 China","institution_ids":[]},{"raw_affiliation_string":"Dept. of Comput. Sci. & Technol., Dalian Neusoft Inst. of Inf., Dalian, China","institution_ids":["https://openalex.org/I4210131997"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044699591","display_name":"Jinying Wu","orcid":"https://orcid.org/0009-0000-2837-5400"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinying Wu","raw_affiliation_strings":["State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101894836","display_name":"Xicheng Wang","orcid":"https://orcid.org/0000-0002-2719-2538"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xicheng Wang","raw_affiliation_strings":["State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, 116023 China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian, China#TAB#","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009811756"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":3.6338,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.93325166,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9789999723434448,"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":0.9789999723434448,"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/T13180","display_name":"Chemistry and Chemical Engineering","score":0.001500000013038516,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12023","display_name":"Cholinesterase and Neurodegenerative Diseases","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8008660674095154},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6376506090164185},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5828027129173279},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4603424370288849},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3839552700519562},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32854291796684265},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1662551462650299},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.13190549612045288},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07513022422790527},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07267585396766663}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8008660674095154},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6376506090164185},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5828027129173279},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4603424370288849},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3839552700519562},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32854291796684265},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1662551462650299},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.13190549612045288},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07513022422790527},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07267585396766663},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13015-015-0034-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0034-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0034-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:25705248","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25705248","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:europepmc.org:3300136","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4336518","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-015-0034-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0034-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0034-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8199999928474426}],"awards":[{"id":"https://openalex.org/G5397225632","display_name":null,"funder_award_id":"B14013","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6233088233","display_name":null,"funder_award_id":"B14013","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G64164466","display_name":null,"funder_award_id":"11202049","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G666444345","display_name":null,"funder_award_id":"2012CB025905","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7015046954","display_name":null,"funder_award_id":"B14013","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G788010770","display_name":null,"funder_award_id":"11202049","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G990389544","display_name":null,"funder_award_id":"2012CB025905","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127358457.pdf","grobid_xml":"https://content.openalex.org/works/W2127358457.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1596348044","https://openalex.org/W1972148009","https://openalex.org/W1973974137","https://openalex.org/W1974809008","https://openalex.org/W1981202673","https://openalex.org/W1985588649","https://openalex.org/W1993403967","https://openalex.org/W2016047921","https://openalex.org/W2035292911","https://openalex.org/W2040496005","https://openalex.org/W2043116111","https://openalex.org/W2050456292","https://openalex.org/W2050992060","https://openalex.org/W2052123709","https://openalex.org/W2055410316","https://openalex.org/W2058252802","https://openalex.org/W2068017935","https://openalex.org/W2080939785","https://openalex.org/W2085315829","https://openalex.org/W2089078246","https://openalex.org/W2092723276","https://openalex.org/W2093426296","https://openalex.org/W2095501702","https://openalex.org/W2098971704","https://openalex.org/W2103300124","https://openalex.org/W2107506448","https://openalex.org/W2110283222","https://openalex.org/W2112101018","https://openalex.org/W2121895929","https://openalex.org/W2125792789","https://openalex.org/W2128332459","https://openalex.org/W2130479394","https://openalex.org/W2133282230","https://openalex.org/W2133773344","https://openalex.org/W2135817448","https://openalex.org/W2151942123","https://openalex.org/W2155524113","https://openalex.org/W2160037672","https://openalex.org/W2160916136","https://openalex.org/W2171234651"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W2417162538","https://openalex.org/W1567411871","https://openalex.org/W2329052364","https://openalex.org/W2162967120","https://openalex.org/W2336040088","https://openalex.org/W2027065525","https://openalex.org/W2773493604","https://openalex.org/W2269591907"],"abstract_inverted_index":{"BACKGROUND:":[0],"As":[1],"a":[2,140,164],"main":[3],"method":[4,104],"of":[5,22,35,64,67,84,98,105,118,143,193],"structure-based":[6],"virtual":[7],"screening,":[8],"molecular":[9,37,46,194],"docking":[10,38,57,132,146,160,167],"is":[11,25,51,77,175],"the":[12,19,28,33,36,56,81,85,95,99,114,121,127,131,135,144,149,181,190],"most":[13],"widely":[14],"used":[15,111,159],"in":[16],"practice.":[17],"However,":[18],"non-ideal":[20],"efficacy":[21],"scoring":[23,61,101,137,186],"functions":[24],"thought":[26],"as":[27,49],"biggest":[29],"barrier":[30],"which":[31,91],"hinders":[32],"improvement":[34],"method.":[39],"RESULTS:":[40],"A":[41],"new":[42],"multi-objective":[43,87,128],"strategy":[44,129,178],"for":[45],"docking,":[47],"named":[48],"MoDock,":[50],"presented":[52],"to":[53,79,112,179],"further":[54],"improve":[55],"accuracy":[58,133],"with":[59,70,148,163],"available":[60],"functions.":[62,102,138],"Instead":[63],"simple":[65],"combination":[66],"multiple":[68],"objectives":[69],"fixed":[71],"weight":[72],"factors,":[73],"an":[74,176],"aggregate":[75],"function":[76],"adopted":[78],"approximate":[80],"real":[82],"solution":[83],"original":[86],"and":[88,107,188],"multi-constraint":[89],"problem,":[90],"will":[92],"simultaneously":[93],"smooth":[94],"energy":[96],"surface":[97],"combined":[100],"Then,":[103],"centers":[106],"genetic":[108],"algorithm":[109],"are":[110],"find":[113],"optimal":[115],"solution.":[116],"Tests":[117],"MoDock":[119,174],"against":[120],"GOLD":[122],"test":[123],"data":[124],"set":[125],"reveal":[126],"improves":[130,189],"over":[134],"individual":[136],"Meanwhile,":[139],"70%":[141],"ratio":[142],"good":[145],"solutions":[147],"RMSD":[150],"value":[151],"below":[152],"1.0":[153],"\u00c5":[154],"outperforms":[155],"other":[156],"6":[157],"commonly":[158],"programs,":[161],"even":[162],"flexible":[165],"receptor":[166],"program":[168],"included.":[169],"CONCLUSIONS:":[170],"The":[171],"results":[172],"show":[173],"effective":[177],"overcome":[180],"deviations":[182],"brought":[183],"by":[184],"single":[185],"function,":[187],"prediction":[191],"power":[192],"docking.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
