{"id":"https://openalex.org/W2180527714","doi":"https://doi.org/10.1093/bioinformatics/btv593","title":"Automatic generation of bioinformatics tools for predicting protein\u2013ligand binding sites","display_name":"Automatic generation of bioinformatics tools for predicting protein\u2013ligand binding sites","publication_year":2015,"publication_date":"2015-11-05","ids":{"openalex":"https://openalex.org/W2180527714","doi":"https://doi.org/10.1093/bioinformatics/btv593","mag":"2180527714","pmid":"https://pubmed.ncbi.nlm.nih.gov/26545824"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv593","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv593","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/901/49018443/bioinformatics_32_6_901.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/32/6/901/49018443/bioinformatics_32_6_901.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080222397","display_name":"Yusuke Komiyama","orcid":"https://orcid.org/0000-0001-6468-3718"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yusuke Komiyama","raw_affiliation_strings":["1 Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan and","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066619074","display_name":"Masaki Banno","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaki Banno","raw_affiliation_strings":["2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090239771","display_name":"Kokoro Ueki","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kokoro Ueki","raw_affiliation_strings":["2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022707734","display_name":"Gul Saad","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Gul Saad","raw_affiliation_strings":["2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102746753","display_name":"Kentaro Shimizu","orcid":"https://orcid.org/0000-0002-3245-0052"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kentaro Shimizu","raw_affiliation_strings":["2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102746753"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7646,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.8599915,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"32","issue":"6","first_page":"901","last_page":"907"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8799999952316284,"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":0.8799999952316284,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.03759999945759773,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.01979999989271164,"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":0.5840427279472351},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5177339911460876},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4124263823032379},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3399474620819092},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23612365126609802}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5840427279472351},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5177339911460876},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4124263823032379},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3399474620819092},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23612365126609802}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":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/btv593","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv593","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/901/49018443/bioinformatics_32_6_901.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:26545824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26545824","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:open-archive.highwire.org:bioinfo:32/6/901","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/6/901","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4803387","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4803387","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv593","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv593","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/901/49018443/bioinformatics_32_6_901.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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G8223820847","display_name":"Development of protein-carbohydrate binding prediction systems and databases","funder_award_id":"23300109","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320327550","display_name":"National Institute of Informatics","ror":"https://ror.org/04ksd4g47"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338078","display_name":"National Bioscience Database Center","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2180527714.pdf","grobid_xml":"https://content.openalex.org/works/W2180527714.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1583240815","https://openalex.org/W1817040532","https://openalex.org/W1831050183","https://openalex.org/W1969142598","https://openalex.org/W1970082412","https://openalex.org/W1977219051","https://openalex.org/W1992972228","https://openalex.org/W2012251953","https://openalex.org/W2018661561","https://openalex.org/W2021312899","https://openalex.org/W2022045489","https://openalex.org/W2024631466","https://openalex.org/W2092146175","https://openalex.org/W2094937489","https://openalex.org/W2096236743","https://openalex.org/W2101234009","https://openalex.org/W2104812418","https://openalex.org/W2105118494","https://openalex.org/W2107903949","https://openalex.org/W2109801072","https://openalex.org/W2118387386","https://openalex.org/W2118976126","https://openalex.org/W2129370330","https://openalex.org/W2130253098","https://openalex.org/W2140538197","https://openalex.org/W2143392414","https://openalex.org/W2144477832","https://openalex.org/W2145126338","https://openalex.org/W2146233784","https://openalex.org/W2151699048","https://openalex.org/W2153026148","https://openalex.org/W2153635508","https://openalex.org/W2157414955","https://openalex.org/W2165428180","https://openalex.org/W2170463736","https://openalex.org/W2170747616","https://openalex.org/W2171149164","https://openalex.org/W2911964244","https://openalex.org/W2916930667","https://openalex.org/W4230932396","https://openalex.org/W6655832863","https://openalex.org/W6675354045","https://openalex.org/W6682299932"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predictive":[1],"tools":[2,30,52,79],"that":[3,31,42],"model":[4],"protein-ligand":[5,49,64],"binding":[6,50,65],"on":[7,130],"demand":[8],"are":[9,116,124,138],"needed":[10],"to":[11,27,35,83],"promote":[12],"ligand":[13,86],"research":[14],"in":[15,71,126],"an":[16],"innovative":[17],"drug-design":[18],"environment.":[19],"However,":[20],"it":[21],"takes":[22],"considerable":[23],"time":[24],"and":[25,45,87,104,113,128],"effort":[26],"develop":[28,47],"predictive":[29,51],"can":[32,43],"be":[33,54],"applied":[34],"individual":[36],"ligands.":[37,106],"An":[38],"automated":[39],"production":[40],"pipeline":[41,73],"rapidly":[44],"efficiently":[46],"user-friendly":[48],"would":[53],"useful.":[55],"RESULTS:":[56],"We":[57,94],"developed":[58],"a":[59,72,85],"system":[60,70],"for":[61,99,119],"automatically":[62],"generating":[63],"predictions.":[66],"Implementation":[67],"of":[68,74],"this":[69],"Semantic":[75],"Web":[76],"technique-based":[77],"web":[78,114],"will":[80],"allow":[81],"users":[82],"specify":[84],"receive":[88],"the":[89],"tool":[90],"within":[91],"0.5-1":[92],"day.":[93],"demonstrated":[95],"high":[96],"prediction":[97],"accuracy":[98],"three":[100],"machine":[101],"learning":[102],"algorithms":[103],"eight":[105],"AVAILABILITY":[107],"AND":[108],"IMPLEMENTATION:":[109],"The":[110],"source":[111],"code":[112],"application":[115],"freely":[117],"available":[118,139],"download":[120],"at":[121,140],"http://utprot.net":[122],"They":[123],"implemented":[125],"Python":[127],"supported":[129],"Linux.":[131],"CONTACT:":[132],"shimizu@bi.a.u-tokyo.ac.jp":[133],"SUPPLEMENTARY":[134],"INFORMATION:":[135],"Supplementary":[136],"data":[137],"Bioinformatics":[141],"online.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
