{"id":"https://openalex.org/W2162825164","doi":"https://doi.org/10.1186/1758-2946-2-s1-p25","title":"Ensemble docking revisited","display_name":"Ensemble docking revisited","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2162825164","doi":"https://doi.org/10.1186/1758-2946-2-s1-p25","mag":"2162825164"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-2-s1-p25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p25","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P25","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P25","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001513198","display_name":"Oliver Korb","orcid":"https://orcid.org/0000-0002-4090-8393"},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Oliver Korb","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013706567","display_name":"Sarah Bowden","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"S Bowden","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058819557","display_name":"Tommy Olsson","orcid":"https://orcid.org/0000-0001-7768-1076"},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"T Olsson","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050049504","display_name":"Daan Frenkel","orcid":"https://orcid.org/0000-0002-6362-2021"},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"D Frenkel","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079380346","display_name":"John W. Liebeschuetz","orcid":"https://orcid.org/0000-0002-1795-1721"},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J Liebeschuetz","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006929803","display_name":"Jason C. Cole","orcid":"https://orcid.org/0000-0002-0291-6317"},"institutions":[{"id":"https://openalex.org/I4210098980","display_name":"Cambridge Crystallographic Data Centre","ror":"https://ror.org/00zbfm828","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210098980"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J Cole","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001513198"],"corresponding_institution_ids":["https://openalex.org/I4210098980"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.0343,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78934039,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9939000010490417,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9886999726295471,"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":0.6574866771697998},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5334005355834961},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35844823718070984},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3548726737499237},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16382119059562683}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6574866771697998},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5334005355834961},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35844823718070984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3548726737499237},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16382119059562683},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-2-s1-p25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p25","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P25","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2867158","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2867158","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-2-s1-p25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p25","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P25","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162825164.pdf","grobid_xml":"https://content.openalex.org/works/W2162825164.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W1973191530","https://openalex.org/W2050456292"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2347219288","https://openalex.org/W2366221835","https://openalex.org/W2608950002","https://openalex.org/W3145628117","https://openalex.org/W2183810260","https://openalex.org/W68685461"],"abstract_inverted_index":{"In":[0],"recent":[1],"years,":[2],"the":[3,19,37,72,94,120,127,136],"importance":[4],"of":[5,40,93,110,119,122,135],"considering":[6],"induced":[7],"fit":[8],"effects":[9],"in":[10,18,32,48,71,117,126],"molecular":[11,20],"docking":[12,35,78],"calculations":[13],"has":[14,82,96],"been":[15,62,83,97],"widely":[16],"recognised":[17],"modelling":[21,39],"community.":[22],"While":[23],"small-scale":[24],"protein":[25,42,69,101,123],"side-chain":[26],"movements":[27,47],"are":[28],"now":[29],"accounted":[30],"for":[31],"many":[33],"state-of-the-art":[34],"strategies,":[36],"explicit":[38],"large-scale":[41],"motions":[43],"such":[44,87],"as":[45],"loop":[46],"kinase":[49],"domains":[50],"is":[51],"still":[52],"a":[53],"challenging":[54],"task.":[55],"For":[56],"this":[57],"reason":[58],"ensemble-based":[59],"methods":[60],"have":[61],"introduced":[63],"taking":[64],"into":[65],"account":[66],"several":[67,100],"discrete":[68],"conformations":[70],"conformational":[73,88,128],"sampling":[74],"step.":[75],"Our":[76],"protein-ligand":[77],"approach":[79,95,137],"GOLD":[80],"[1,2]":[81],"extended":[84],"to":[85],"search":[86],"ensembles":[89],"time-efficiently.":[90],"The":[91],"performance":[92],"assessed":[98],"on":[99],"targets":[102],"using":[103],"different":[104],"scoring":[105],"functions.":[106],"A":[107],"detailed":[108],"analysis":[109],"pose":[111],"prediction":[112],"and":[113,133],"virtual":[114],"screening":[115],"results":[116],"dependence":[118],"number":[121],"structures":[124],"considered":[125],"ensemble":[129],"will":[130,138],"be":[131,139],"presented":[132],"limitations":[134],"highlighted.":[140]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
