{"id":"https://openalex.org/W2032993192","doi":"https://doi.org/10.1109/bibe.2012.6399684","title":"Binding site extraction by similar subgraphs mining from protein molecular surfaces","display_name":"Binding site extraction by similar subgraphs mining from protein molecular surfaces","publication_year":2012,"publication_date":"2012-11-01","ids":{"openalex":"https://openalex.org/W2032993192","doi":"https://doi.org/10.1109/bibe.2012.6399684","mag":"2032993192"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2012.6399684","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5020610628","display_name":"Natsumi Kurumatani","orcid":null},"institutions":[{"id":"https://openalex.org/I65837984","display_name":"Kobe University","ror":"https://ror.org/03tgsfw79","country_code":"JP","type":"education","lineage":["https://openalex.org/I65837984"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Natsumi Kurumatani","raw_affiliation_strings":["Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","institution_ids":["https://openalex.org/I65837984"]},{"raw_affiliation_string":"Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan","institution_ids":["https://openalex.org/I65837984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039037668","display_name":"Hiroyuki Monji","orcid":null},"institutions":[{"id":"https://openalex.org/I65837984","display_name":"Kobe University","ror":"https://ror.org/03tgsfw79","country_code":"JP","type":"education","lineage":["https://openalex.org/I65837984"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroyuki Monji","raw_affiliation_strings":["Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","institution_ids":["https://openalex.org/I65837984"]},{"raw_affiliation_string":"Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan","institution_ids":["https://openalex.org/I65837984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108699952","display_name":"Takenao Ohkawa","orcid":"https://orcid.org/0000-0002-5745-0956"},"institutions":[{"id":"https://openalex.org/I65837984","display_name":"Kobe University","ror":"https://ror.org/03tgsfw79","country_code":"JP","type":"education","lineage":["https://openalex.org/I65837984"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takenao Ohkawa","raw_affiliation_strings":["Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of System Informatics, Kobe University, Nada, Kobe, Japan","institution_ids":["https://openalex.org/I65837984"]},{"raw_affiliation_string":"Graduate School of System Informatics Kobe University 1\u20101 Rokkodai, Nada Kobe 657\u20108501 Japan","institution_ids":["https://openalex.org/I65837984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020610628"],"corresponding_institution_ids":["https://openalex.org/I65837984"],"apc_list":null,"apc_paid":null,"fwci":0.1313,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.50900719,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"255","last_page":"259"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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":0.9987999796867371,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9950000047683716,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9950000047683716,"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/binding-site","display_name":"Binding site","score":0.7476800084114075},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.546267569065094},{"id":"https://openalex.org/keywords/surface-protein","display_name":"Surface protein","score":0.4711165428161621},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4470071494579315},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.42678138613700867},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.39672738313674927},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.345893919467926},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32692039012908936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2992725372314453},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19610488414764404},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1897551417350769},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.10512033104896545}],"concepts":[{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.7476800084114075},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.546267569065094},{"id":"https://openalex.org/C3019232848","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Surface protein","level":2,"score":0.4711165428161621},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4470071494579315},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.42678138613700867},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39672738313674927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.345893919467926},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32692039012908936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2992725372314453},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19610488414764404},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1897551417350769},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.10512033104896545},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2012.6399684","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1517566065","https://openalex.org/W1579899614","https://openalex.org/W1926568554","https://openalex.org/W1997803213","https://openalex.org/W2019951137","https://openalex.org/W2031772330","https://openalex.org/W2040074453","https://openalex.org/W2101654328","https://openalex.org/W2112109058","https://openalex.org/W2139942857","https://openalex.org/W2147932348","https://openalex.org/W2163839956","https://openalex.org/W2168491690"],"related_works":["https://openalex.org/W2355466661","https://openalex.org/W1968459159","https://openalex.org/W1972166651","https://openalex.org/W4287836304","https://openalex.org/W2075669521","https://openalex.org/W3184847642","https://openalex.org/W4238460368","https://openalex.org/W4385689227","https://openalex.org/W2000376957","https://openalex.org/W2025584407"],"abstract_inverted_index":{"Most":[0],"proteins":[1,9,82,117,204],"express":[2],"their":[3],"functions":[4,85],"by":[5,98,148],"binding":[6,20,24,30,45,87,96,126,177,213],"with":[7,83],"other":[8],"or":[10],"molecular":[11],"compounds":[12],"called":[13,22,72,131],"ligands.":[14],"The":[15,26],"local":[16],"portion":[17],"involved":[18],"in":[19,107,185],"is":[21],"a":[23,92,109,114,187,200],"site.":[25],"characteristics":[27],"of":[28,36,43,47,54,94,116,170,202,205,212,224],"the":[29,34,37,41,44,48,52,77,100,121,133,145,154,164,168,175,225],"site":[31,46,88,214],"often":[32,63],"determine":[33],"function":[35,53],"protein,":[38],"so":[39],"clarifying":[40],"location":[42],"protein":[49],"helps":[50],"analyze":[51],"proteins.":[55,172],"Binding":[56],"sites":[57,97,127,178],"that":[58,103,118],"bind":[59,119],"to":[60,120,143,153,162,189,199],"similar":[61,84,150],"ligands":[62],"have":[64,128],"common":[65,69,138,176],"surface":[66,73,78,101,146],"structures.":[67],"Such":[68],"structures":[70,130,139],"are":[71,104,135,140,158],"motifs.":[74],"Therefore,":[75],"extracting":[76,99],"motifs":[79,102,147],"among":[80,167],"several":[81,171,180],"improves":[86],"prediction.":[89],"We":[90],"propose":[91],"method":[93,198],"predicting":[95],"frequently":[105],"observed":[106],"only":[108],"specific":[110],"group,":[111],"which":[112,157],"means":[113],"set":[115,201],"same":[122],"ligand.":[123],"Since":[124],"most":[125],"concave":[129],"pockets,":[132],"pockets":[134,169],"compared":[136],"and":[137,218,230],"searched":[141],"for":[142,220],"extract":[144],"applying":[149],"graph":[151],"mining":[152],"pocket":[155],"data,":[156],"represented":[159],"as":[160],"graphs,":[161],"find":[163],"frequent":[165],"subgraphs":[166],"In":[173],"addition,":[174],"across":[179],"groups":[181,226],"can":[182],"be":[183],"predicted":[184],"such":[186],"way":[188],"integrate":[190],"more":[191,221],"than":[192,222],"one":[193],"group.":[194],"Applying":[195],"our":[196],"proposed":[197],"37":[203],"five":[206],"groups,":[207],"we":[208],"achieved":[209],"success":[210],"rates":[211],"prediction":[215],"over":[216],"40%":[217],"50%":[219],"half":[223],"without":[227],"group":[228],"integration":[229],"using":[231],"integration,":[232],"respectively.":[233]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}