{"id":"https://openalex.org/W2207671224","doi":"https://doi.org/10.1021/ci050382y","title":"Alignment-Free Classification of G-Protein-Coupled Receptors Using Self-Organizing Maps","display_name":"Alignment-Free Classification of G-Protein-Coupled Receptors Using Self-Organizing Maps","publication_year":2006,"publication_date":"2006-04-05","ids":{"openalex":"https://openalex.org/W2207671224","doi":"https://doi.org/10.1021/ci050382y","mag":"2207671224","pmid":"https://pubmed.ncbi.nlm.nih.gov/16711767"},"language":"en","primary_location":{"id":"doi:10.1021/ci050382y","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050382y","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/A5041964842","display_name":"Joji M. Otaki","orcid":"https://orcid.org/0000-0003-3425-7085"},"institutions":[{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Joji M. Otaki","raw_affiliation_strings":["Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan","institution_ids":["https://openalex.org/I41802502"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011467015","display_name":"Akihito Mori","orcid":null},"institutions":[{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akihito Mori","raw_affiliation_strings":["Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan","institution_ids":["https://openalex.org/I41802502"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038022681","display_name":"Yoshimasa Itoh","orcid":null},"institutions":[{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshimasa Itoh","raw_affiliation_strings":["Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan","institution_ids":["https://openalex.org/I41802502"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103205935","display_name":"Takashi Nakayama","orcid":"https://orcid.org/0009-0002-3008-1684"},"institutions":[{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takashi Nakayama","raw_affiliation_strings":["Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan","institution_ids":["https://openalex.org/I41802502"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111801231","display_name":"Haruhiko Yamamoto","orcid":null},"institutions":[{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Haruhiko Yamamoto","raw_affiliation_strings":["Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Department of Information and Computer Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan","institution_ids":["https://openalex.org/I41802502"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.091,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.76064292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"46","issue":"3","first_page":"1479","last_page":"1490"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9983000159263611,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9983000159263611,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9975000023841858,"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":0.9872999787330627,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/g-protein-coupled-receptor","display_name":"G protein-coupled receptor","score":0.5782507061958313},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5044888257980347},{"id":"https://openalex.org/keywords/self-organizing-map","display_name":"Self-organizing map","score":0.44422924518585205},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44227397441864014},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42468297481536865},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4061243534088135},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.39147454500198364},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.32733476161956787},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31097549200057983},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12928631901741028}],"concepts":[{"id":"https://openalex.org/C135285700","wikidata":"https://www.wikidata.org/wiki/Q38173","display_name":"G protein-coupled receptor","level":3,"score":0.5782507061958313},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5044888257980347},{"id":"https://openalex.org/C111168008","wikidata":"https://www.wikidata.org/wiki/Q1136838","display_name":"Self-organizing map","level":3,"score":0.44422924518585205},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44227397441864014},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42468297481536865},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4061243534088135},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.39147454500198364},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.32733476161956787},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31097549200057983},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12928631901741028}],"mesh":[{"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":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019204","descriptor_name":"GTP-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019204","descriptor_name":"GTP-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019204","descriptor_name":"GTP-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci050382y","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050382y","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:16711767","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16711767","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":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323550","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W577199904","https://openalex.org/W1968240641","https://openalex.org/W1987303875","https://openalex.org/W1998684744","https://openalex.org/W2002566401","https://openalex.org/W2005162839","https://openalex.org/W2010671788","https://openalex.org/W2012851563","https://openalex.org/W2019074781","https://openalex.org/W2023306209","https://openalex.org/W2024213882","https://openalex.org/W2033801097","https://openalex.org/W2038422963","https://openalex.org/W2053877769","https://openalex.org/W2060321728","https://openalex.org/W2076074498","https://openalex.org/W2076776559","https://openalex.org/W2077583250","https://openalex.org/W2080412532","https://openalex.org/W2083566192","https://openalex.org/W2084430953","https://openalex.org/W2105416365","https://openalex.org/W2107427637","https://openalex.org/W2111010158","https://openalex.org/W2118866905","https://openalex.org/W2149963584","https://openalex.org/W2157959080","https://openalex.org/W2165665320","https://openalex.org/W4233523656","https://openalex.org/W4245176872","https://openalex.org/W4300052965","https://openalex.org/W4388293083"],"related_works":["https://openalex.org/W1485085181","https://openalex.org/W1864425659","https://openalex.org/W1967231335","https://openalex.org/W2386387936","https://openalex.org/W1970046535","https://openalex.org/W2031950886","https://openalex.org/W2269979065","https://openalex.org/W2063998199","https://openalex.org/W3049725047","https://openalex.org/W2474749047"],"abstract_inverted_index":{"Proteins":[0],"are":[1],"classified":[2,96,135],"mainly":[3],"on":[4,17],"the":[5,36,138,141,152,157,173,198,203],"basis":[6],"of":[7,9,54,63,74,86,90,115,140,148,169,202],"alignments":[8],"amino":[10],"acid":[11],"sequences.":[12,38,214],"Drug":[13],"discovery":[14,211],"processes":[15],"based":[16],"pharmacologically":[18],"important":[19],"proteins":[20,64],"such":[21],"as":[22,190],"G-protein-coupled":[23],"receptors":[24,150,186],"(GPCRs)":[25],"may":[26],"be":[27,95,176],"facilitated":[28],"if":[29],"more":[30],"information":[31],"is":[32],"extracted":[33],"directly":[34],"from":[35,212],"primary":[37,61],"Here,":[39],"we":[40],"investigate":[41],"an":[42,77],"alignment-free":[43],"approach":[44],"to":[45,178,206],"protein":[46,213],"classification":[47,207],"using":[48,137],"self-organizing":[49],"maps":[50],"(SOMs),":[51],"a":[52,71,84,109,128],"kind":[53,171],"artificial":[55],"neural":[56],"network,":[57],"which":[58],"needs":[59],"only":[60],"sequences":[62],"and":[65,161,200,209],"determines":[66],"their":[67],"relative":[68],"locations":[69],"in":[70,127,156,172],"two-dimensional":[72],"lattice":[73],"neurons":[75],"through":[76],"adaptive":[78],"process.":[79],"We":[80],"first":[81],"showed":[82],"that":[83,187],"set":[85,114],"1397":[87],"aligned":[88],"samples":[89,117],"Class":[91],"A":[92,144,167],"GPCRs":[93,132],"can":[94,175],"by":[97],"our":[98],"SOM":[99,142,204],"program":[100,205],"into":[101,120],"15":[102,121],"conventional":[103,122],"categories":[104],"with":[105,124],"99.2%":[106],"accuracy.":[107],"Similarly,":[108],"nonaligned":[110],"raw":[111],"sequence":[112],"data":[113],"4116":[116],"was":[118],"categorized":[119,189],"families":[123,163],"97.8%":[125],"accuracy":[126],"cross-validation":[129],"test.":[130],"Orphan":[131],"were":[133,188,192],"also":[134],"appropriately":[136],"result":[139],"learning.":[143],"supposedly":[145],"diverse":[146],"family":[147,181],"olfactory":[149,191],"formed":[151],"most":[153],"distinctive":[154],"cluster":[155],"map,":[158],"whereas":[159],"amine":[160],"peptide":[162],"exhibited":[164],"diffuse":[165],"distributions.":[166],"feature":[168],"this":[170],"map":[174],"interpreted":[177],"reflect":[179],"hierarchical":[180],"composition.":[182],"Interestingly,":[183],"some":[184],"orphan":[185],"somatosensory":[193],"chemoreceptors.":[194],"These":[195],"results":[196],"suggest":[197],"applicability":[199],"potential":[201],"prediction":[208],"knowledge":[210]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}