{"id":"https://openalex.org/W2140678125","doi":"https://doi.org/10.1093/bioinformatics/bth370","title":"Comparison of probabilistic combination methods for protein secondary structure prediction","display_name":"Comparison of probabilistic combination methods for protein secondary structure prediction","publication_year":2004,"publication_date":"2004-06-24","ids":{"openalex":"https://openalex.org/W2140678125","doi":"https://doi.org/10.1093/bioinformatics/bth370","mag":"2140678125","pmid":"https://pubmed.ncbi.nlm.nih.gov/15217817"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3099/48906425/bioinformatics_20_17_3099.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/20/17/3099/48906425/bioinformatics_20_17_3099.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100351175","display_name":"Yan Liu","orcid":"https://orcid.org/0000-0003-4242-4840"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yan Liu","raw_affiliation_strings":["Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA. yanliu@cs.cmu.edu","Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA. yanliu@cs.cmu.edu","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108407140","display_name":"Jaime G. Carbonell","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaime Carbonell","raw_affiliation_strings":["Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065265042","display_name":"Judith Klein\u2010Seetharaman","orcid":"https://orcid.org/0000-0002-4892-6828"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Judith Klein-Seetharaman","raw_affiliation_strings":["Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069347895","display_name":"Vanathi Gopalakrishnan","orcid":"https://orcid.org/0000-0002-7813-4055"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vanathi Gopalakrishnan","raw_affiliation_strings":["Center for Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA15260, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA15260, USA#TAB#","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100351175"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2052,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.77291631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"20","issue":"17","first_page":"3099","last_page":"3107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9217000007629395,"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":0.9217000007629395,"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":0.020099999383091927,"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":0.01730000041425228,"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.6062139272689819},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5682045221328735},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.43008726835250854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38218581676483154},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36280936002731323},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3028373122215271},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17635592818260193}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6062139272689819},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5682045221328735},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.43008726835250854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38218581676483154},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36280936002731323},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3028373122215271},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17635592818260193},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":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":"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":"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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":"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:10.1093/bioinformatics/bth370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3099/48906425/bioinformatics_20_17_3099.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:15217817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15217817","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:10.1.1.188.3804","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.188.3804","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.cmu.edu/%7Ejgc/publication/Comparison_Probabilistic_Combination_Bioinformatics_2004.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.214.340","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.214.340","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.cmu.edu/%7Eyanliu/papers/BIOINF_2004_0763.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.318.598","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.318.598","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/20/17/3099.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3099/48906425/bioinformatics_20_17_3099.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":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1504694836","https://openalex.org/W1934019294","https://openalex.org/W1969621320","https://openalex.org/W1977324596","https://openalex.org/W1985818354","https://openalex.org/W2008708467","https://openalex.org/W2041369927","https://openalex.org/W2053621743","https://openalex.org/W2057289558","https://openalex.org/W2081856012","https://openalex.org/W2087894810","https://openalex.org/W2100890997","https://openalex.org/W2104972430","https://openalex.org/W2119571185","https://openalex.org/W2122945697","https://openalex.org/W2125055259","https://openalex.org/W2125838338","https://openalex.org/W2131801377","https://openalex.org/W2137329336","https://openalex.org/W2139193890","https://openalex.org/W2139582206","https://openalex.org/W2140244239","https://openalex.org/W2147880316","https://openalex.org/W2147905080","https://openalex.org/W2153187042","https://openalex.org/W2156798505","https://openalex.org/W2156909104","https://openalex.org/W2157046483","https://openalex.org/W2158441306","https://openalex.org/W2994982620"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834","https://openalex.org/W1975122118","https://openalex.org/W1564749278","https://openalex.org/W2294851134"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"secondary":[2,28,76,129],"structure":[3,77,130],"prediction":[4,60],"is":[5],"an":[6],"important":[7],"step":[8],"towards":[9],"understanding":[10],"how":[11],"proteins":[12],"fold":[13],"in":[14,74],"three":[15],"dimensions.":[16],"Recent":[17],"analysis":[18],"by":[19],"information":[20],"theory":[21],"indicates":[22],"that":[23,34,93],"the":[24,45,52,63,88,100,112,124],"correlation":[25],"between":[26],"neighboring":[27,36],"structures":[29],"are":[30,95,123],"much":[31],"stronger":[32],"than":[33,99],"of":[35,65],"amino":[37],"acids.":[38],"In":[39,104],"this":[40],"article,":[41],"we":[42],"focus":[43],"on":[44],"combination":[46,89],"problem":[47,90],"for":[48,72,114,119,127],"sequences,":[49],"i.e.":[50],"combining":[51],"scores":[53],"or":[54,58],"assignments":[55],"from":[56],"single":[57],"multiple":[59],"systems":[61],"under":[62],"constraint":[64],"a":[66,70],"whole":[67],"sequence,":[68],"as":[69],"target":[71],"improvement":[73],"protein":[75,128],"prediction.":[78,131],"RESULTS:":[79],"We":[80],"apply":[81],"several":[82],"graphical":[83],"chain":[84],"models":[85],"to":[86],"solve":[87],"and":[91],"show":[92],"they":[94],"consistently":[96],"more":[97,117],"effective":[98],"traditional":[101],"window-based":[102],"methods.":[103],"particular,":[105],"conditional":[106],"random":[107],"fields":[108],"(CRFs)":[109],"moderately":[110],"improve":[111],"predictions":[113],"helices":[115],"and,":[116],"importantly,":[118],"beta":[120],"sheets,":[121],"which":[122],"major":[125],"bottleneck":[126]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}