{"id":"https://openalex.org/W2096252784","doi":"https://doi.org/10.1186/1471-2105-13-233","title":"Automatic classification of protein structures relying on similarities between alignments","display_name":"Automatic classification of protein structures relying on similarities between alignments","publication_year":2012,"publication_date":"2012-09-14","ids":{"openalex":"https://openalex.org/W2096252784","doi":"https://doi.org/10.1186/1471-2105-13-233","mag":"2096252784","pmid":"https://pubmed.ncbi.nlm.nih.gov/22974051"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-233","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-233","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075097983","display_name":"Guillaume Santini","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091279","display_name":"Universit\u00e9 Sorbonne Paris Nord","ror":"https://ror.org/0199hds37","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210091279"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210156583","display_name":"Laboratoire d'Informatique de Paris-Nord","ror":"https://ror.org/05g1zjw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210091279","https://openalex.org/I4210156583","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210159731","display_name":"LIP6","ror":"https://ror.org/05krcen59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210159245","https://openalex.org/I4210159731"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Guillaume Santini","raw_affiliation_strings":["Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d'Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France. guillaume.santini@lipn.univ-paris13.fr","Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d\u2019Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d'Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France. guillaume.santini@lipn.univ-paris13.fr","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4210156583","https://openalex.org/I4210159731"]},{"raw_affiliation_string":"Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d\u2019Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4210156583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000152441","display_name":"Henry Soldano","orcid":"https://orcid.org/0000-0001-8505-948X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210091279","display_name":"Universit\u00e9 Sorbonne Paris Nord","ror":"https://ror.org/0199hds37","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210091279"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210156583","display_name":"Laboratoire d'Informatique de Paris-Nord","ror":"https://ror.org/05g1zjw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210091279","https://openalex.org/I4210156583","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Henry Soldano","raw_affiliation_strings":["UPMC, Universit\u00e9 Paris 06, Atelier de BioInformatique, F-75005, Paris, France","Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d\u2019Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UPMC, Universit\u00e9 Paris 06, Atelier de BioInformatique, F-75005, Paris, France","institution_ids":["https://openalex.org/I39804081"]},{"raw_affiliation_string":"Universit\u00e9 Paris 13, Sorbonne Paris Cit\u00e9, Laboratoire d\u2019Informatique de Paris-Nord (LIPN), CNRS(, UMR 7030), Villetaneuse, F-93430, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4210156583"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055217500","display_name":"Jo\u00ebl Pothier","orcid":"https://orcid.org/0000-0002-4021-6055"},"institutions":[{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jo\u00ebl Pothier","raw_affiliation_strings":["UPMC, Universit\u00e9 Paris 06, Atelier de BioInformatique, F-75005, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UPMC, Universit\u00e9 Paris 06, Atelier de BioInformatique, F-75005, Paris, France","institution_ids":["https://openalex.org/I39804081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5075097983"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4210156583","https://openalex.org/I4210159731"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4909,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.630165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"13","issue":"1","first_page":"233","last_page":"233"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6352999806404114,"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":0.6352999806404114,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.09449999779462814,"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/T11162","display_name":"Enzyme Structure and Function","score":0.06480000168085098,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.6323661804199219},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5731329917907715},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5283328294754028},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4871232509613037},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.444113165140152},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2591990828514099}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6323661804199219},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5731329917907715},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5283328294754028},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4871232509613037},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.444113165140152},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2591990828514099}],"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-13-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-233","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22974051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22974051","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:95289dd64ac44c6b98e799bca9f13862","is_oa":false,"landing_page_url":"https://doaj.org/article/95289dd64ac44c6b98e799bca9f13862","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 13, Iss 1, p 233 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2537176","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3534633","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3534633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3534633","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-233","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096252784.pdf","grobid_xml":"https://content.openalex.org/works/W2096252784.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1585080294","https://openalex.org/W1965910641","https://openalex.org/W1972969203","https://openalex.org/W1976526581","https://openalex.org/W2002850151","https://openalex.org/W2004308928","https://openalex.org/W2007186548","https://openalex.org/W2016381774","https://openalex.org/W2021495307","https://openalex.org/W2027305455","https://openalex.org/W2033047894","https://openalex.org/W2062318714","https://openalex.org/W2091535494","https://openalex.org/W2115312817","https://openalex.org/W2120189049","https://openalex.org/W2124166542","https://openalex.org/W2128653811","https://openalex.org/W2130479394","https://openalex.org/W2132122858","https://openalex.org/W2133657429","https://openalex.org/W2141805605","https://openalex.org/W2143205129","https://openalex.org/W2147758638","https://openalex.org/W2151785844","https://openalex.org/W2165874743","https://openalex.org/W2745750801","https://openalex.org/W2912046975","https://openalex.org/W4237496336"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identification":[1],"of":[2,8,10,17,23,28,47,50,57,72,89,144,169,181,222,245,316,318,328],"protein":[3,31,97,106,202,278],"structural":[4,18,78,114],"cores":[5],"requires":[6],"isolation":[7],"sets":[9,49],"proteins":[11,112,317],"all":[12],"sharing":[13],"a":[14,55,77,87,92,95,120,127,142,151,163,167,173,184,212,226,243,265,286],"same":[15,140],"subset":[16,143],"motifs.":[19],"In":[20,154],"the":[21,69,139,179,199,219,250,254,262,314,325,336],"context":[22],"an":[24,100],"ever":[25],"growing":[26],"number":[27],"available":[29],"3D":[30,58,96,105,145,170,291],"structures,":[32,59],"standard":[33,266,302,329],"and":[34,99,224,257,321],"automatic":[35],"clustering":[36,122,134,268,305,332],"algorithms":[37,135,333],"require":[38],"adaptations":[39],"so":[40,194],"as":[41,63,119,172,195],"to":[42,68,156,175,196,241,248,253,259,261,301,335],"allow":[43],"for":[44,274,289],"efficient":[45],"identification":[46],"such":[48,126],"proteins.":[51],"RESULTS:":[52],"When":[53],"considering":[54],"pair":[56],"they":[60],"are":[61,108,234],"stated":[62],"similar":[64],"or":[65],"not":[66,149],"according":[67,252,334],"local":[70],"similarities":[71,90,190,223,283,299],"their":[73],"matching":[74],"substructures":[75],"in":[76,86,138,229],"alignment.":[79],"This":[80],"binary":[81],"relation":[82],"can":[83,116],"be":[84,117,176],"represented":[85],"graph":[88,121,128,180,221,228,244,251,264,267,303,330],"where":[91],"node":[93],"represents":[94],"structure":[98,292],"edge":[101],"states":[102],"that":[103,147,198,215,297],"two":[104],"structures":[107,146,171,203],"similar.":[109],"Therefore,":[110],"classifying":[111,275],"into":[113,188],"families":[115],"viewed":[118],"task.":[123],"Unfortunately,":[124],"because":[125],"encodes":[129],"only":[130],"pairwise":[131,192,282],"similarity":[132,165,310],"information,":[133],"may":[136],"include":[137],"cluster":[141],"do":[148,204],"share":[150],"common":[152,207],"substructure.":[153,208],"order":[155],"overcome":[157],"this":[158],"drawback":[159],"we":[160],"first":[161,240],"define":[162],"ternary":[164,185,232,309],"on":[166],"triple":[168],"constraint":[174,186],"satisfied":[177],"by":[178,307],"similarities.":[182],"Such":[183,270],"takes":[187],"account":[189],"between":[191],"alignments,":[193],"ensure":[197],"three":[200],"involved":[201],"have":[205],"some":[206],"We":[209,295],"propose":[210],"hereunder":[211],"modification":[213,255],"algorithm":[214],"eliminates":[216],"edges":[217],"from":[218],"original":[220],"gives":[225],"reduced":[227,263],"which":[230],"no":[231],"constraints":[233,311],"violated.":[235],"Our":[236],"approach":[237],"is":[238],"then":[239,247],"build":[242],"similarities,":[246],"reduce":[249],"algorithm,":[256],"finally":[258],"apply":[260],"algorithm.":[269],"method":[271],"was":[272],"used":[273],"ASTRAL-40":[276],"non-redundant":[277],"domains,":[279],"identifying":[280],"significant":[281],"with":[284],"Yakusa,":[285],"program":[287],"devised":[288],"rapid":[290],"alignments.":[293],"CONCLUSIONS:":[294],"show":[296],"filtering":[298],"prior":[300],"based":[304,331],"process":[306],"applying":[308],"i)":[312],"improves":[313,324],"separation":[315],"different":[319],"classes":[320],"consequently":[322],"ii)":[323],"classification":[326,338],"quality":[327],"reference":[337],"SCOP.":[339]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
