{"id":"https://openalex.org/W2147145103","doi":"https://doi.org/10.1093/bioinformatics/bts213","title":"A conditional neural fields model for protein threading","display_name":"A conditional neural fields model for protein threading","publication_year":2012,"publication_date":"2012-06-09","ids":{"openalex":"https://openalex.org/W2147145103","doi":"https://doi.org/10.1093/bioinformatics/bts213","mag":"2147145103","pmid":"https://pubmed.ncbi.nlm.nih.gov/22689779"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts213","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts213","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i59/48883601/bioinformatics_28_12_i59.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/28/12/i59/48883601/bioinformatics_28_12_i59.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074269040","display_name":"Jianzhu Ma","orcid":"https://orcid.org/0000-0002-8236-6609"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jianzhu Ma","raw_affiliation_strings":["Toyota Technological Institute at Chicago IL 60637, USA","Toyota Technological Institute at Chicago, IL 60637 USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]},{"raw_affiliation_string":"Toyota Technological Institute at Chicago, IL 60637 USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047373240","display_name":"Jian Peng","orcid":"https://orcid.org/0000-0002-1820-4015"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jian Peng","raw_affiliation_strings":["Toyota Technological Institute at Chicago IL 60637, USA","Toyota Technological Institute at Chicago, IL 60637 USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]},{"raw_affiliation_string":"Toyota Technological Institute at Chicago, IL 60637 USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371324","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0003-4210-1670"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sheng Wang","raw_affiliation_strings":["Toyota Technological Institute at Chicago IL 60637, USA","Toyota Technological Institute at Chicago, IL 60637 USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]},{"raw_affiliation_string":"Toyota Technological Institute at Chicago, IL 60637 USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Toyota Technological Institute at Chicago IL 60637, USA","Toyota Technological Institute at Chicago, IL 60637 USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]},{"raw_affiliation_string":"Toyota Technological Institute at Chicago, IL 60637 USA","institution_ids":["https://openalex.org/I160992636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074269040"],"corresponding_institution_ids":["https://openalex.org/I160992636"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.496,"has_fulltext":true,"cited_by_count":100,"citation_normalized_percentile":{"value":0.93561451,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"28","issue":"12","first_page":"i59","last_page":"i66"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"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":0.9970999956130981,"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/threading","display_name":"Threading (protein sequence)","score":0.8856216669082642},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7140551209449768},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.6304140686988831},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5317636132240295},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5131948590278625},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.48959001898765564},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.4767683148384094},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46693840622901917},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45981842279434204},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44789865612983704},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.43749138712882996},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43242546916007996},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3679802119731903},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3657190203666687},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3573210835456848},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.18199977278709412},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1779557764530182},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11277318000793457}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.8856216669082642},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7140551209449768},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.6304140686988831},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5317636132240295},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5131948590278625},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.48959001898765564},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.4767683148384094},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46693840622901917},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45981842279434204},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44789865612983704},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.43749138712882996},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43242546916007996},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3679802119731903},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3657190203666687},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3573210835456848},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.18199977278709412},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1779557764530182},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11277318000793457},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"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":"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":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":"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":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts213","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts213","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i59/48883601/bioinformatics_28_12_i59.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:22689779","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22689779","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:europepmc.org:2378065","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3371845","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts213","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts213","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i59/48883601/bioinformatics_28_12_i59.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":[{"id":"https://openalex.org/G2229035017","display_name":null,"funder_award_id":"R01GM089753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4673750664","display_name":null,"funder_award_id":"DBI-0960390","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5777097233","display_name":null,"funder_award_id":"R01GM0897532","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309626","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147145103.pdf","grobid_xml":"https://content.openalex.org/works/W2147145103.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1493248875","https://openalex.org/W1578951231","https://openalex.org/W1611898338","https://openalex.org/W1623871094","https://openalex.org/W1629279812","https://openalex.org/W1967538863","https://openalex.org/W1967695819","https://openalex.org/W1978304263","https://openalex.org/W1984586858","https://openalex.org/W1991133427","https://openalex.org/W2003852785","https://openalex.org/W2004228538","https://openalex.org/W2004575181","https://openalex.org/W2008016457","https://openalex.org/W2008708467","https://openalex.org/W2022058405","https://openalex.org/W2036149515","https://openalex.org/W2051434435","https://openalex.org/W2051969447","https://openalex.org/W2060791849","https://openalex.org/W2066142272","https://openalex.org/W2073895233","https://openalex.org/W2082667898","https://openalex.org/W2084466582","https://openalex.org/W2086765355","https://openalex.org/W2102245393","https://openalex.org/W2105961968","https://openalex.org/W2108435962","https://openalex.org/W2109502170","https://openalex.org/W2112284439","https://openalex.org/W2112380236","https://openalex.org/W2118851904","https://openalex.org/W2124776405","https://openalex.org/W2126064524","https://openalex.org/W2126131681","https://openalex.org/W2126159149","https://openalex.org/W2130357646","https://openalex.org/W2140181132","https://openalex.org/W2140244239","https://openalex.org/W2141022852","https://openalex.org/W2141885858","https://openalex.org/W2142529984","https://openalex.org/W2143210482","https://openalex.org/W2143739717","https://openalex.org/W2144472358","https://openalex.org/W2144483796","https://openalex.org/W2145010684","https://openalex.org/W2145371840","https://openalex.org/W2145541064","https://openalex.org/W2147880316","https://openalex.org/W2153153865","https://openalex.org/W2158714788","https://openalex.org/W2159545104","https://openalex.org/W2160672912","https://openalex.org/W2161062388","https://openalex.org/W2161151688","https://openalex.org/W2912451784","https://openalex.org/W4210400672","https://openalex.org/W6634635036","https://openalex.org/W6670511902","https://openalex.org/W6676382333","https://openalex.org/W6678583454","https://openalex.org/W6681840848"],"related_works":["https://openalex.org/W2253761889","https://openalex.org/W2411998238","https://openalex.org/W2462594639","https://openalex.org/W4311623193","https://openalex.org/W1504467230","https://openalex.org/W2043066834","https://openalex.org/W2266510186","https://openalex.org/W2398461637","https://openalex.org/W2034313881","https://openalex.org/W4387310732"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,17,22,37,48,92],"novel":[3,93],"protein":[4,30,51,177],"threading":[5,88,126],"method,":[6,95,101],"CNFpred,":[7],"which":[8,27],"achieves":[9],"much":[10,72],"more":[11,73],"accurate":[12],"sequence-template":[13],"alignment":[14],"by":[15],"employing":[16],"probabilistic":[18],"graphical":[19],"model":[20],"called":[21],"Conditional":[23],"Neural":[24],"Field":[25],"(CNF),":[26],"aligns":[28],"one":[29],"sequence":[31,52,160,178],"to":[32,66,102,163,176],"its":[33],"remote":[34],"template":[35],"using":[36],"non-linear":[38],"scoring":[39,42,82],"function.":[40,83],"This":[41],"function":[43],"accounts":[44],"for":[45,156],"correlation":[46],"among":[47],"variety":[49],"of":[50,58,63,97,108,145,150,167],"and":[53,69,125,152],"structure":[54,168],"features,":[55],"makes":[56],"use":[57],"information":[59],"in":[60],"the":[61,76,98,105,109,122,146,164],"neighborhood":[62],"two":[64],"residues":[65],"be":[67,174],"aligned,":[68],"is":[70],"thus":[71],"sensitive":[74],"than":[75,121],"widely":[77],"used":[78],"linear":[79],"or":[80,148],"profile-based":[81,124],"To":[84],"train":[85],"this":[86],"CNF":[87],"model,":[89],"we":[90],"employ":[91],"quality-sensitive":[94],"instead":[96],"standard":[99],"maximum-likelihood":[100],"maximize":[103],"directly":[104],"expected":[106],"quality":[107],"training":[110],"set.":[111],"Experimental":[112],"results":[113],"show":[114],"that":[115],"CNFpred":[116,141],"generates":[117],"significantly":[118],"better":[119],"alignments":[120],"best":[123],"methods":[127],"on":[128],"several":[129],"public":[130],"(but":[131],"small)":[132],"benchmarks":[133],"as":[134,136],"well":[135,155],"our":[137],"own":[138],"large":[139],"dataset.":[140],"outperforms":[142],"others":[143],"regardless":[144],"lengths":[147],"classes":[149],"proteins,":[151],"works":[153],"particularly":[154],"proteins":[157],"with":[158],"sparse":[159],"profiles":[161],"due":[162],"effective":[165],"utilization":[166],"information.":[169],"Our":[170],"methodology":[171],"can":[172],"also":[173],"adapted":[175],"alignment.":[179]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
