{"id":"https://openalex.org/W1579875912","doi":"https://doi.org/10.1186/1758-2946-5-s1-o7","title":"How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening","display_name":"How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W1579875912","doi":"https://doi.org/10.1186/1758-2946-5-s1-o7","mag":"1579875912"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-s1-o7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-o7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-O7","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","license_id":"https://openalex.org/licenses/cc-by","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/10.1186/1758-2946-5-S1-O7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001909059","display_name":"Barbara Sander","orcid":null},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Barbara Sander","raw_affiliation_strings":["School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK","School of Chemistry, University of Southampton, Highfield, UK"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK","institution_ids":["https://openalex.org/I43439940"]},{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, UK","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"middle","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":false,"raw_author_name":"Oliver Korb","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","Cambridge Crystallographic Data Centre, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]},{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, Cambridge, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"middle","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":"Jason Cole","raw_affiliation_strings":["Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","Cambridge Crystallographic Data Centre, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK","institution_ids":["https://openalex.org/I4210098980"]},{"raw_affiliation_string":"Cambridge Crystallographic Data Centre, Cambridge, UK","institution_ids":["https://openalex.org/I4210098980"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067820273","display_name":"Jonathan W. Essex","orcid":"https://orcid.org/0000-0003-2639-2746"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan W Essex","raw_affiliation_strings":["School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK","School of Chemistry, University of Southampton, Highfield, UK"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK","institution_ids":["https://openalex.org/I43439940"]},{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, UK","institution_ids":["https://openalex.org/I43439940"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5001909059"],"corresponding_institution_ids":["https://openalex.org/I43439940"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.3736,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61683077,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","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":0.9984999895095825,"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":0.9984999895095825,"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":0.9968000054359436,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9914000034332275,"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/virtual-screening","display_name":"Virtual screening","score":0.8047906756401062},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7180932760238647},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.6276236176490784},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4123914837837219},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3708495497703552},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34606635570526123},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33824533224105835},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2934444546699524},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22063302993774414},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07885691523551941}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8047906756401062},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7180932760238647},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6276236176490784},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4123914837837219},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3708495497703552},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34606635570526123},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33824533224105835},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2934444546699524},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22063302993774414},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07885691523551941}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-5-s1-o7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-o7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-O7","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2605496","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3606248","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:10.1186/1758-2946-5-s1-o7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-o7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-O7","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6800000071525574,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1579875912.pdf","grobid_xml":"https://content.openalex.org/works/W1579875912.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2004967944","https://openalex.org/W2019732485","https://openalex.org/W2084485490"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4224009465","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W3046775127","https://openalex.org/W4205958290","https://openalex.org/W3107474891","https://openalex.org/W3209574120","https://openalex.org/W3170094116"],"abstract_inverted_index":{"The":[0,27,103],"necessity":[1],"of":[2,17,23,29,59,71,87,92,129,144,198,210,226],"treating":[3],"receptor":[4],"flexibility":[5],"in":[6,20,49,77,158,213],"protein-ligand":[7],"docking":[8,50,99,148,159,186],"has":[9,37],"been":[10,38,135],"widely":[11],"acknowledged":[12],"and":[13,107,124,137,149,224],"is":[14,66],"the":[15,21,57,78,170,177,196,214,237],"subject":[16],"extensive":[18],"research":[19],"field":[22],"drug":[24],"discovery":[25],"[1].":[26],"use":[28],"multiple":[30],"discrete":[31],"protein":[32,110,171],"conformations,":[33],"so-called":[34],"ensemble":[35],"docking,":[36],"proven":[39],"to":[40,45],"be":[41,64,75,95,113,174,189,221,230],"a":[42,116,142,192],"valid":[43],"concept":[44],"mimic":[46],"target":[47],"plasticity":[48],"experiments":[51,152],"[2,3].":[52],"Using":[53],"molecular":[54,130],"dynamics":[55,131],"(MD)":[56],"number":[58],"different":[60],"conformations":[61,73,111,200],"that":[62,154],"can":[63,74,112,188,220,229],"generated":[65],"practically":[67],"unlimited.":[68],"Not":[69],"all":[70],"these":[72],"included":[76],"pose":[79],"prediction":[80],"or":[81],"virtual":[82,150,203,217],"screening":[83,151,218],"process":[84],"for":[85,98,201],"reasons":[86],"computational":[88],"cost.":[89],"Moreover,":[90],"some":[91],"them":[93],"will":[94],"more":[96],"suitable":[97,199],"purposes":[100],"than":[101],"others.":[102],"question":[104],"arises":[105],"if":[106],"how":[108],"adequate":[109],"selected":[114],"systematically":[115],"priori":[117],"based":[118],"on":[119],"quantifiable":[120],"structural":[121],"features.\r\n\r\nFor":[122],"neuraminidase":[123],"cyclin-dependent":[125],"kinase":[126],"II,":[127],"snapshots":[128,228],"simulation":[132],"trajectories":[133],"have":[134],"clustered":[136],"structurally":[138],"assessed":[139],"by":[140,163,176],"applying":[141],"variety":[143],"methods.":[145,181],"Extensive":[146],"cross":[147,185],"show":[153],"relatively":[155],"large":[156],"differences":[157],"performance":[160,219],"are":[161],"caused":[162],"only":[164],"very":[165],"subtle":[166],"conformational":[167],"changes":[168],"within":[169],"which":[172,232],"cannot":[173],"captured":[175],"currently":[178],"applied":[179],"characterisation":[180],"As":[182],"an":[183],"alternative,":[184],"capability":[187],"used":[190],"as":[191,234,236],"reliable":[193],"indicator":[194],"towards":[195],"selection":[197],"ensemble-based":[202],"screening.":[204],"In":[205],"combination":[206],"with":[207],"short":[208],"minimisations":[209],"docked":[211],"poses":[212],"binding":[215],"site,":[216],"further":[222],"improved":[223],"ensembles":[225],"MD":[227],"built":[231],"perform":[233],"well":[235],"generally":[238],"superior":[239],"holo":[240],"crystal":[241],"structures.":[242]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}