{"id":"https://openalex.org/W2968836630","doi":"https://doi.org/10.1093/bioinformatics/btz642","title":"LightDock goes information-driven","display_name":"LightDock goes information-driven","publication_year":2019,"publication_date":"2019-08-15","ids":{"openalex":"https://openalex.org/W2968836630","doi":"https://doi.org/10.1093/bioinformatics/btz642","mag":"2968836630","pmid":"https://pubmed.ncbi.nlm.nih.gov/31418773"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/950/48982918/bioinformatics_36_3_950.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/950/48982918/bioinformatics_36_3_950.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086790564","display_name":"Jorge Roel\u2010Touris","orcid":"https://orcid.org/0000-0002-6588-624X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jorge Roel-Touris","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-6588-624X","affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Alexandre M J J Bonvin","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0001-7369-1322","affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012374366","display_name":"Brian Jim\u00e9nez\u2010Garc\u00eda","orcid":"https://orcid.org/0000-0001-7786-2109"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Brian Jim\u00e9nez-Garc\u00eda","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012374366"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.4409,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.82014105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"3","first_page":"950","last_page":"952"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5896999835968018,"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":0.5896999835968018,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.13050000369548798,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.03830000013113022,"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/docking","display_name":"Docking (animal)","score":0.7845700979232788},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7728582620620728},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.562131404876709},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5547938942909241},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5219364166259766},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5211731791496277},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08351624011993408}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7845700979232788},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7728582620620728},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.562131404876709},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5547938942909241},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5219364166259766},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5211731791496277},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08351624011993408},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","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},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/950/48982918/bioinformatics_36_3_950.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31418773","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31418773","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:pubmedcentral.nih.gov:7005597","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7005597","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/391766","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/391766","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 36(3). Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/950/48982918/bioinformatics_36_3_950.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1109448040","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G140804232","display_name":"Centre of Excellence for Biomolecular Research","funder_award_id":"675728","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3471917844","display_name":"BioExcel Centre of Excellence for ComputationalBiomolecular Research","funder_award_id":"823830","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4562669","display_name":"Caught in the act: a combined magnetic resonance -modelling approach to capture cellular machines at work","funder_award_id":"718.015.001","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G604989270","display_name":null,"funder_award_id":"675728","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G7172891301","display_name":"Integrating and managing services for the European Open Science Cloud","funder_award_id":"777536","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2968836630.pdf","grobid_xml":"https://content.openalex.org/works/W2968836630.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1978496023","https://openalex.org/W1988972583","https://openalex.org/W2027403155","https://openalex.org/W2053538195","https://openalex.org/W2064660701","https://openalex.org/W2081912151","https://openalex.org/W2125677968","https://openalex.org/W2136777954","https://openalex.org/W2153983456","https://openalex.org/W2163194931","https://openalex.org/W2753374271","https://openalex.org/W2799682268"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W2087343574","https://openalex.org/W4230315250"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,140],"use":[2,20],"of":[3,14,81,99,107,116],"experimental":[4,34],"information":[5,21,58],"has":[6],"been":[7],"demonstrated":[8],"to":[9,22,68,132],"increase":[10],"the":[11,24,30,64,69,74,97,103,108],"success":[12],"rate":[13],"computational":[15],"macromolecular":[16],"docking.":[17,136],"Many":[18],"methods":[19],"post-filter":[23],"simulation":[25,31],"output":[26],"while":[27],"others":[28],"drive":[29],"based":[32,90],"on":[33,91,102],"restraints,":[35],"which":[36],"can":[37],"become":[38],"problematic":[39],"for":[40,55,78],"more":[41],"complex":[42],"scenarios":[43],"such":[44],"as":[45],"multiple":[46],"binding":[47],"interfaces.":[48],"RESULTS:":[49],"We":[50,95],"present":[51],"a":[52,124],"novel":[53],"method":[54],"including":[56],"interface":[57],"into":[59],"protein":[60],"docking":[61],"simulations":[62],"within":[63],"LightDock":[65],"framework.":[66],"Prior":[67],"simulation,":[70],"irrelevant":[71],"regions":[72],"from":[73,147,152],"receptor":[75],"are":[76,88,158],"excluded":[77],"sampling":[79],"(filter":[80],"initial":[82,85],"swarms)":[83],"and":[84,144,149],"ligand":[86,92],"poses":[87],"pre-oriented":[89],"input":[93],"information.":[94,117],"demonstrate":[96],"applicability":[98],"this":[100],"approach":[101],"new":[104],"55":[105],"cases":[106],"Protein-Protein":[109],"Docking":[110],"Benchmark":[111],"5,":[112],"using":[113],"different":[114],"amounts":[115],"Even":[118],"with":[119],"incomplete":[120],"or":[121],"incorrect":[122],"information,":[123],"significant":[125],"improvement":[126],"in":[127],"performance":[128],"is":[129,142],"obtained":[130],"compared":[131],"blind":[133],"ab":[134],"initio":[135],"AVAILABILITY":[137],"AND":[138],"IMPLEMENTATION:":[139],"software":[141],"supported":[143],"freely":[145],"available":[146,159],"https://github.com/brianjimenez/lightdock":[148],"analysis":[150],"data":[151,157],"https://github.com/brianjimenez/lightdock_bm5.":[153],"SUPPLEMENTARY":[154],"INFORMATION:":[155],"Supplementary":[156],"at":[160],"Bioinformatics":[161],"online.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
