{"id":"https://openalex.org/W2081201773","doi":"https://doi.org/10.1021/ci1000289","title":"Large-Scale Comparison of Four Binding Site Detection Algorithms","display_name":"Large-Scale Comparison of Four Binding Site Detection Algorithms","publication_year":2010,"publication_date":"2010-09-09","ids":{"openalex":"https://openalex.org/W2081201773","doi":"https://doi.org/10.1021/ci1000289","mag":"2081201773","pmid":"https://pubmed.ncbi.nlm.nih.gov/20828173"},"language":"en","primary_location":{"id":"doi:10.1021/ci1000289","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci1000289","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035587835","display_name":"Peter Schmidtke","orcid":"https://orcid.org/0000-0003-3172-3669"},"institutions":[{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I3018075036","display_name":"Sanofi (France)","ror":"https://ror.org/02n6c9837","country_code":"FR","type":"company","lineage":["https://openalex.org/I3018075036"]}],"countries":["ES","FR"],"is_corresponding":true,"raw_author_name":"Peter Schmidtke","raw_affiliation_strings":["Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I3018075036"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086891705","display_name":"Catherine Souaille","orcid":null},"institutions":[{"id":"https://openalex.org/I3018075036","display_name":"Sanofi (France)","ror":"https://ror.org/02n6c9837","country_code":"FR","type":"company","lineage":["https://openalex.org/I3018075036"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES","FR"],"is_corresponding":false,"raw_author_name":"Catherine Souaille","raw_affiliation_strings":["Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I3018075036"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022414793","display_name":"Fr\u00e9d\u00e9ric Estienne","orcid":null},"institutions":[{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I3018075036","display_name":"Sanofi (France)","ror":"https://ror.org/02n6c9837","country_code":"FR","type":"company","lineage":["https://openalex.org/I3018075036"]}],"countries":["ES","FR"],"is_corresponding":false,"raw_author_name":"Fr\u00e9d\u00e9ric Estienne","raw_affiliation_strings":["Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I3018075036"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036757314","display_name":"Nicolas Baurin","orcid":null},"institutions":[{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I3018075036","display_name":"Sanofi (France)","ror":"https://ror.org/02n6c9837","country_code":"FR","type":"company","lineage":["https://openalex.org/I3018075036"]}],"countries":["ES","FR"],"is_corresponding":false,"raw_author_name":"Nicolas Baurin","raw_affiliation_strings":["Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I3018075036"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054733198","display_name":"Romano T. Kroemer","orcid":null},"institutions":[{"id":"https://openalex.org/I3018075036","display_name":"Sanofi (France)","ror":"https://ror.org/02n6c9837","country_code":"FR","type":"company","lineage":["https://openalex.org/I3018075036"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES","FR"],"is_corresponding":false,"raw_author_name":"Romano T. Kroemer","raw_affiliation_strings":["Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France and Departament de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I3018075036"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5035587835"],"corresponding_institution_ids":["https://openalex.org/I3018075036","https://openalex.org/I71999127"],"apc_list":null,"apc_paid":null,"fwci":7.3304,"has_fulltext":false,"cited_by_count":89,"citation_normalized_percentile":{"value":0.97597648,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"50","issue":"12","first_page":"2191","last_page":"2200"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9641000032424927,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9641000032424927,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T12923","display_name":"Digital Image Processing Techniques","score":0.9474999904632568,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/scale","display_name":"Scale (ratio)","score":0.5476627349853516},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4768846333026886},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3937831521034241},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.13484063744544983},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.09130746126174927}],"concepts":[{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5476627349853516},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4768846333026886},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3937831521034241},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.13484063744544983},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.09130746126174927}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci1000289","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci1000289","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:20828173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20828173","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1517566065","https://openalex.org/W1965910641","https://openalex.org/W1994067196","https://openalex.org/W1994921798","https://openalex.org/W2001143464","https://openalex.org/W2018408116","https://openalex.org/W2019971393","https://openalex.org/W2022058405","https://openalex.org/W2025458374","https://openalex.org/W2030650909","https://openalex.org/W2031194866","https://openalex.org/W2031290814","https://openalex.org/W2045591342","https://openalex.org/W2050330741","https://openalex.org/W2058463742","https://openalex.org/W2066143642","https://openalex.org/W2088013021","https://openalex.org/W2089085945","https://openalex.org/W2091563009","https://openalex.org/W2096039340","https://openalex.org/W2097642323","https://openalex.org/W2105902442","https://openalex.org/W2112109058","https://openalex.org/W2115177539","https://openalex.org/W2122300808","https://openalex.org/W2124789466","https://openalex.org/W2126609920","https://openalex.org/W2144714500","https://openalex.org/W2146224808","https://openalex.org/W2164088236","https://openalex.org/W2204075485","https://openalex.org/W3023233709"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"A":[0],"large-scale":[1],"evaluation":[2],"and":[3,18,31,70,107,116,151],"comparison":[4],"of":[5,39,61,89,98,118,142],"four":[6,54],"cavity":[7],"detection":[8],"algorithms":[9,14,55,133],"was":[10,78],"carried":[11],"out.":[12],"The":[13,123],"SiteFinder,":[15,65],"fpocket,":[16],"PocketFinder,":[17],"SiteMap":[19,150],"were":[20],"evaluated":[21,134],"on":[22,86],"a":[23,37,58],"protein":[24],"test":[25],"set":[26,41],"containing":[27],"5416":[28],"protein-ligand":[29],"complexes":[30],"9900":[32],"apo":[33,103],"forms,":[34],"corresponding":[35],"to":[36],"subset":[38],"the":[40,46,50,82,90,94,99,102,132],"used":[42],"earlier":[43],"for":[44,149,155],"benchmarking":[45],"PocketFinder":[47,105],"algorithm.":[48],"For":[49],"holo":[51],"structures,":[52,104],"all":[53,119],"correctly":[56],"identified":[57],"similar":[59,73],"amount":[60],"pockets":[62],"(around":[63],"95%).":[64],"using":[66],"optimized":[67],"parameters,":[68],"SiteMap,":[69],"fpocket":[71,124],"showed":[72],"pocket":[74],"ranking":[75,81],"performance,":[76],"which":[77],"defined":[79],"by":[80],"correct":[83],"binding":[84,120,127],"site":[85],"rank":[87],"1":[88],"predictions":[91],"or":[92],"within":[93],"first":[95],"5":[96],"ranks":[97],"predictions.":[100],"On":[101],"especially":[106],"also":[108],"SiteFinder":[109,136],"(optimized":[110],"parameters)":[111],"performed":[112],"best,":[113],"identifying":[114],"96%":[115],"84%":[117],"sites,":[121],"respectively.":[122],"program":[125],"predicts":[126],"sites":[128],"most":[129],"accurately":[130],"among":[131],"here.":[135],"needed":[137],"an":[138],"average":[139],"calculation":[140],"time":[141],"1.6":[143],"s":[144,154],"compared":[145],"with":[146],"2":[147,153],"min":[148],"around":[152],"fpocket.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":11}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
