{"id":"https://openalex.org/W2116751407","doi":"https://doi.org/10.1093/bioinformatics/bth062","title":"A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins","display_name":"A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins","publication_year":2004,"publication_date":"2004-01-20","ids":{"openalex":"https://openalex.org/W2116751407","doi":"https://doi.org/10.1093/bioinformatics/bth062","mag":"2116751407","pmid":"https://pubmed.ncbi.nlm.nih.gov/14534176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth062","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/293/534081/bth062.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/20/2/293/534081/bth062.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022568938","display_name":"Torgeir R. Hvidsten","orcid":"https://orcid.org/0000-0001-6097-2539"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Torgeir R. Hvidsten","raw_affiliation_strings":["The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I223464139","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046112262","display_name":"Andriy Kryshtafovych","orcid":"https://orcid.org/0000-0001-5066-7178"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andriy Kryshtafovych","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jan Komorowski","raw_affiliation_strings":["Uppsala University ,"],"affiliations":[{"raw_affiliation_string":"Uppsala University ,","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074974770","display_name":"Krzysztof Fidelis","orcid":"https://orcid.org/0000-0002-8061-412X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Krzysztof Fidelis","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022568938"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I223464139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4033,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.79702017,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"2","first_page":"293","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9957000017166138,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9947999715805054,"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/sequence","display_name":"Sequence (biology)","score":0.7202712297439575},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.7008644342422485},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.61017245054245},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.5191285014152527},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.4735549986362457},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.46015292406082153},{"id":"https://openalex.org/keywords/loop-modeling","display_name":"Loop modeling","score":0.4506511688232422},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4491559565067291},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42449212074279785},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.42206305265426636},{"id":"https://openalex.org/keywords/identity","display_name":"Identity (music)","score":0.4184757471084595},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.40731361508369446},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3860839903354645},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34405896067619324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.326541930437088},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.3111375570297241},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10589134693145752},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09686657786369324},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09300759434700012}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7202712297439575},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.7008644342422485},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.61017245054245},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.5191285014152527},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.4735549986362457},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.46015292406082153},{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.4506511688232422},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4491559565067291},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42449212074279785},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.42206305265426636},{"id":"https://openalex.org/C2778355321","wikidata":"https://www.wikidata.org/wiki/Q17079427","display_name":"Identity (music)","level":2,"score":0.4184757471084595},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.40731361508369446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3860839903354645},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34405896067619324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.326541930437088},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3111375570297241},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10589134693145752},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09686657786369324},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09300759434700012},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"D017510","descriptor_name":"Protein Folding","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":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth062","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/293/534081/bth062.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:14534176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14534176","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/bth062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth062","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/293/534081/bth062.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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116751407.pdf","grobid_xml":"https://content.openalex.org/works/W2116751407.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1970197953","https://openalex.org/W1982446140","https://openalex.org/W1983572327","https://openalex.org/W1990698302","https://openalex.org/W1995945562","https://openalex.org/W1999181825","https://openalex.org/W2000231698","https://openalex.org/W2000629283","https://openalex.org/W2002592134","https://openalex.org/W2003853681","https://openalex.org/W2011495938","https://openalex.org/W2020898453","https://openalex.org/W2026258231","https://openalex.org/W2028231353","https://openalex.org/W2033496784","https://openalex.org/W2040644205","https://openalex.org/W2044128233","https://openalex.org/W2051721370","https://openalex.org/W2062957518","https://openalex.org/W2073693914","https://openalex.org/W2088083202","https://openalex.org/W2093717447","https://openalex.org/W2109109045","https://openalex.org/W2111696858","https://openalex.org/W2117500290","https://openalex.org/W2130479394","https://openalex.org/W2135338271","https://openalex.org/W2145358391","https://openalex.org/W2150627302","https://openalex.org/W2153187042","https://openalex.org/W2154106236","https://openalex.org/W2157825442","https://openalex.org/W2158714788","https://openalex.org/W2160879227","https://openalex.org/W2161896699","https://openalex.org/W2163295140"],"related_works":["https://openalex.org/W2088487249","https://openalex.org/W2015399150","https://openalex.org/W1971751969","https://openalex.org/W1493920382","https://openalex.org/W2398461637","https://openalex.org/W2414840205","https://openalex.org/W2026882519","https://openalex.org/W2157930580","https://openalex.org/W2121560377","https://openalex.org/W2140187548"],"abstract_inverted_index":{"Comparative":[0],"modeling":[1],"methods":[2,68],"can":[3],"consistently":[4],"produce":[5],"reliable":[6],"structural":[7,38,42],"models":[8],"for":[9,118],"protein":[10,173],"sequences":[11,31,120,130],"with":[12,20,32,87,165],"more":[13],"than":[14,167],"25%":[15],"sequence":[16,34,85,94,163,169],"identity":[17,35,170],"to":[18,97,103,113,171,175],"proteins":[19],"known":[21],"structure.":[22],"However,":[23],"there":[24],"is":[25],"a":[26,49,78,160],"good":[27],"chance":[28],"that":[29,69],"also":[30],"lower":[33],"have":[36,131,141],"their":[37,136],"components":[39],"represented":[40],"in":[41,145],"databases.":[43],"To":[44],"this":[45],"end,":[46],"we":[47,76],"present":[48],"novel":[50],"fragment-based":[51,67],"method":[52],"using":[53],"sets":[54,83],"of":[55,60,80,84,110,128,147,162],"structurally":[56],"similar":[57,89],"local":[58,90],"fragments":[59,86],"proteins.":[61],"The":[62],"approach":[63,112,154],"differs":[64],"from":[65,121],"other":[66],"use":[70,77],"only":[71],"single":[72],"backbone":[73],"fragments.":[74],"Instead,":[75],"library":[79],"groups":[81],"containing":[82],"geometrically":[88],"structures":[91],"and":[92],"extract":[93],"related":[95],"properties":[96],"assign":[98],"these":[99,129],"specific":[100],"geometrical":[101],"conformations":[102],"target":[104],"sequences.":[105],"We":[106],"test":[107],"the":[108,111,122,132,142,148,153,177],"ability":[109],"recognize":[114],"correct":[115,133,143],"SCOP":[116],"folds":[117],"273":[119],"49":[123],"most":[124],"popular":[125],"folds.":[126],"49%":[127],"fold":[134,144],"as":[135],"top":[137,149],"prediction,":[138],"while":[139],"82%":[140],"one":[146],"five":[150],"predictions.":[151],"Moreover,":[152],"shows":[155],"no":[156],"performance":[157],"reduction":[158],"on":[159],"subset":[161],"targets":[164],"less":[166],"10%":[168],"any":[172],"used":[174],"build":[176],"library.":[178]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
