{"id":"https://openalex.org/W2170002939","doi":"https://doi.org/10.1093/bioinformatics/btr654","title":"SCPC: a method to structurally compare protein complexes","display_name":"SCPC: a method to structurally compare protein complexes","publication_year":2011,"publication_date":"2011-11-29","ids":{"openalex":"https://openalex.org/W2170002939","doi":"https://doi.org/10.1093/bioinformatics/btr654","mag":"2170002939","pmid":"https://pubmed.ncbi.nlm.nih.gov/22130591"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/324/48875053/bioinformatics_28_3_324.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/324/48875053/bioinformatics_28_3_324.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088515417","display_name":"Ryotaro Koike","orcid":"https://orcid.org/0000-0003-2965-6954"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryotaro Koike","raw_affiliation_strings":["Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004774267","display_name":"Motonori Ota","orcid":"https://orcid.org/0000-0001-9090-668X"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Motonori Ota","raw_affiliation_strings":["Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5088515417"],"corresponding_institution_ids":["https://openalex.org/I60134161"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2623,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.59465273,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"28","issue":"3","first_page":"324","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.616100013256073,"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":0.616100013256073,"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/T12094","display_name":"Hemoglobin structure and function","score":0.12229999899864197,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11162","display_name":"Enzyme Structure and Function","score":0.07779999822378159,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5124123692512512},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.366025447845459},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34744349122047424},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19052717089653015}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5124123692512512},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.366025447845459},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34744349122047424},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19052717089653015}],"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":"D006454","descriptor_name":"Hemoglobins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006454","descriptor_name":"Hemoglobins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006454","descriptor_name":"Hemoglobins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/324/48875053/bioinformatics_28_3_324.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22130591","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22130591","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/324/48875053/bioinformatics_28_3_324.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1510161841","https://openalex.org/W1965910641","https://openalex.org/W1973695911","https://openalex.org/W1976261957","https://openalex.org/W1977186059","https://openalex.org/W1977845138","https://openalex.org/W1979249349","https://openalex.org/W1983544779","https://openalex.org/W1993273781","https://openalex.org/W2000377676","https://openalex.org/W2004194157","https://openalex.org/W2015292449","https://openalex.org/W2018712093","https://openalex.org/W2022058405","https://openalex.org/W2024431726","https://openalex.org/W2025157802","https://openalex.org/W2028231353","https://openalex.org/W2035007496","https://openalex.org/W2037442572","https://openalex.org/W2039063819","https://openalex.org/W2044322490","https://openalex.org/W2046986600","https://openalex.org/W2052039588","https://openalex.org/W2058123092","https://openalex.org/W2060554354","https://openalex.org/W2065304353","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2101060075","https://openalex.org/W2102245393","https://openalex.org/W2109872885","https://openalex.org/W2117510107","https://openalex.org/W2122863289","https://openalex.org/W2128674962","https://openalex.org/W2130687290","https://openalex.org/W2137796207","https://openalex.org/W2142513984","https://openalex.org/W2144998676","https://openalex.org/W2148830024","https://openalex.org/W2152326664","https://openalex.org/W2152653671","https://openalex.org/W2158714788","https://openalex.org/W2161899160","https://openalex.org/W2167869241","https://openalex.org/W2916767477","https://openalex.org/W2917375902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","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"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein-protein":[1],"interactions":[2],"play":[3],"vital":[4],"functional":[5],"roles":[6],"in":[7,41,81,86,97,134],"various":[8],"biological":[9],"phenomena.":[10],"Physical":[11],"contacts":[12],"between":[13,119],"proteins":[14],"have":[15,22,58],"been":[16],"revealed":[17],"using":[18,89,150],"experimental":[19],"approaches":[20],"that":[21,50,161],"solved":[23],"the":[24,34,42,76,102,120,155,169],"structures":[25,147,170],"of":[26,37,62,79,141,145,148,171],"protein":[27,38,52,72,99,172],"complexes":[28,39,53,100],"at":[29,178,188],"atomic":[30],"resolution.":[31],"To":[32],"examine":[33],"huge":[35],"number":[36],"available":[40,177,187],"Protein":[43,63],"Data":[44],"Bank,":[45],"an":[46,126],"efficient":[47],"automated":[48],"method":[49,68],"compares":[51,75],"is":[54,104,163,176],"required.":[55],"RESULTS:":[56],"We":[57],"developed":[59],"Structural":[60],"Comparison":[61],"Complexes":[64],"(SCPC),":[65],"a":[66,82,135,138,164],"novel":[67],"to":[69,109,167],"structurally":[70],"compare":[71],"complexes.":[73,173],"SCPC":[74,106,114,151,162,175],"spatial":[77],"arrangements":[78],"subunits":[80],"complex":[83,88],"with":[84,154],"those":[85],"another":[87],"secondary":[90],"structure":[91],"elements.":[92],"Similar":[93],"substructures":[94,131],"are":[95,186],"detected":[96,133],"two":[98],"and":[101,112,137],"similarity":[103],"scored.":[105],"was":[107,152],"applied":[108],"dimers,":[110],"homo-oligomers":[111],"haemoglobins.":[113],"properly":[115],"estimated":[116],"structural":[117],"similarities":[118],"dimers":[121],"examined":[122],"as":[123,125],"well":[124],"existing":[127],"method,":[128],"MM-align.":[129],"Conserved":[130],"were":[132],"homo-tetramer":[136],"homo-hexamer":[139],"composed":[140],"homologous":[142],"proteins.":[143],"Classification":[144],"quaternary":[146],"haemoglobins":[149],"consistent":[153],"conventional":[156],"classification.":[157],"The":[158],"results":[159],"demonstrate":[160],"valuable":[165],"tool":[166],"investigate":[168],"AVAILABILITY:":[174],"http://idp1.force.cs.is.nagoya-u.ac.jp/scpc/.":[179],"CONTACT:":[180],"rkoike@is.nagoya-u.ac.jp":[181],"SUPPLEMENTARY":[182],"INFORMATION:":[183],"Supplementary":[184],"data":[185],"Bioinformatics":[189],"online.":[190]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
