{"id":"https://openalex.org/W2101756156","doi":"https://doi.org/10.1093/bioinformatics/btp474","title":"Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments","display_name":"Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments","publication_year":2009,"publication_date":"2009-08-10","ids":{"openalex":"https://openalex.org/W2101756156","doi":"https://doi.org/10.1093/bioinformatics/btp474","mag":"2101756156","pmid":"https://pubmed.ncbi.nlm.nih.gov/19667079"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp474","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp474","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057508937","display_name":"Pin-Hao Chi","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pin-Hao Chi","raw_affiliation_strings":["1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101969689","display_name":"Bin Pang","orcid":"https://orcid.org/0000-0003-0298-2047"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Pang","raw_affiliation_strings":["1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022192689","display_name":"Dmitry Korkin","orcid":"https://orcid.org/0000-0002-3875-9085"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitry Korkin","raw_affiliation_strings":["1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013031415","display_name":"Chi\u2010Ren Shyu","orcid":"https://orcid.org/0000-0001-9197-9522"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi-Ren Shyu","raw_affiliation_strings":["1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"1 Medical and Biological Digital Library Research Lab, Informatics Institute and 2Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057508937"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5391,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66995768,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"25","issue":"19","first_page":"2559","last_page":"2565"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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":0.998199999332428,"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/substructure","display_name":"Substructure","score":0.6734362840652466},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6585277318954468},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6066602468490601},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.5427361726760864},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4846647381782532},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.41808193922042847},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3605191707611084},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35519346594810486},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33527177572250366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1826358139514923},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11764630675315857}],"concepts":[{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.6734362840652466},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6585277318954468},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6066602468490601},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.5427361726760864},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4846647381782532},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.41808193922042847},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3605191707611084},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35519346594810486},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33527177572250366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1826358139514923},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11764630675315857},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, 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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp474","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp474","pdf_url":null,"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:19667079","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19667079","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:CiteSeerX.psu:10.1.1.937.4798","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.937.4798","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/08/10/bioinformatics.btp474.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309568","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1489843519","https://openalex.org/W1491063910","https://openalex.org/W1503558940","https://openalex.org/W1520321564","https://openalex.org/W1774934401","https://openalex.org/W1955025754","https://openalex.org/W1965910641","https://openalex.org/W1966190762","https://openalex.org/W1971650367","https://openalex.org/W1976287380","https://openalex.org/W1979147581","https://openalex.org/W2016685072","https://openalex.org/W2022058405","https://openalex.org/W2049540991","https://openalex.org/W2053281575","https://openalex.org/W2085277871","https://openalex.org/W2096540816","https://openalex.org/W2099698841","https://openalex.org/W2115177539","https://openalex.org/W2115451817","https://openalex.org/W2118447204","https://openalex.org/W2118851904","https://openalex.org/W2124358359","https://openalex.org/W2126016150","https://openalex.org/W2128055227","https://openalex.org/W2130479394","https://openalex.org/W2135338271","https://openalex.org/W2136567909","https://openalex.org/W2138546444","https://openalex.org/W2144998676","https://openalex.org/W2151430326","https://openalex.org/W2151785844","https://openalex.org/W2152326664","https://openalex.org/W2155072429","https://openalex.org/W2157092487","https://openalex.org/W2157242929","https://openalex.org/W2163016858","https://openalex.org/W2168211076","https://openalex.org/W4210870538","https://openalex.org/W4290750029","https://openalex.org/W6630003107","https://openalex.org/W6631239882","https://openalex.org/W6644525740","https://openalex.org/W6680654961","https://openalex.org/W6681619517","https://openalex.org/W6682969285"],"related_works":["https://openalex.org/W3153444835","https://openalex.org/W2153916713","https://openalex.org/W2023846184","https://openalex.org/W2703419385","https://openalex.org/W2329056228","https://openalex.org/W2284584236","https://openalex.org/W1979083399","https://openalex.org/W2374530195","https://openalex.org/W2953357932","https://openalex.org/W2393932274"],"abstract_inverted_index":{"IPSA":[0],"is":[1],"publicly":[2],"accessible":[3],"at":[4],"http://ProteinDBS.rnet.missouri.edu/IPSA.php":[5]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
