{"id":"https://openalex.org/W1936662467","doi":"https://doi.org/10.1371/journal.pcbi.1003500","title":"MRFalign: Protein Homology Detection through Alignment of Markov Random Fields","display_name":"MRFalign: Protein Homology Detection through Alignment of Markov Random Fields","publication_year":2014,"publication_date":"2014-03-27","ids":{"openalex":"https://openalex.org/W1936662467","doi":"https://doi.org/10.1371/journal.pcbi.1003500","mag":"1936662467","pmid":"https://pubmed.ncbi.nlm.nih.gov/24675572"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003500","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003500","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003500&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003500&type=printable","any_repository_has_fulltext":true},"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":false,"raw_author_name":"Jianzhu Ma","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America","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, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100443929","display_name":"Zhiyong Wang","orcid":"https://orcid.org/0000-0002-5326-6537"},"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":"Zhiyong Wang","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America","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":true,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I160992636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019398608"],"corresponding_institution_ids":["https://openalex.org/I160992636"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.0254,"has_fulltext":true,"cited_by_count":99,"citation_normalized_percentile":{"value":0.96175135,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"3","first_page":"e1003500","last_page":"e1003500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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":0.9977999925613403,"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":0.9930999875068665,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.9104949235916138},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6533958315849304},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.6500462293624878},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6205050945281982},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5391896367073059},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5324723720550537},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5314623117446899},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.530811071395874},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.5282807946205139},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4803772568702698},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4771042466163635},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4692136347293854},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.43994495272636414},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.42082154750823975},{"id":"https://openalex.org/keywords/markov-random-field","display_name":"Markov random field","score":0.41675445437431335},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3226468563079834},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3115761876106262},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3031398057937622},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29030174016952515},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15394997596740723},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15389683842658997},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.07127916812896729},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.05969312787055969}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.9104949235916138},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6533958315849304},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.6500462293624878},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6205050945281982},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5391896367073059},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5324723720550537},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5314623117446899},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.530811071395874},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.5282807946205139},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4803772568702698},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4771042466163635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4692136347293854},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.43994495272636414},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.42082154750823975},{"id":"https://openalex.org/C2778045648","wikidata":"https://www.wikidata.org/wiki/Q176827","display_name":"Markov random field","level":4,"score":0.41675445437431335},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3226468563079834},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3115761876106262},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3031398057937622},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29030174016952515},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15394997596740723},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15389683842658997},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.07127916812896729},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.05969312787055969},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","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":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003500","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003500","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003500&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:24675572","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24675572","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:arXiv.org:1401.2668","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1401.2668","pdf_url":"https://arxiv.org/pdf/1401.2668","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003500","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003500","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:5af7307a47024e8695343ecfb15b8e60","is_oa":true,"landing_page_url":"https://doaj.org/article/5af7307a47024e8695343ecfb15b8e60","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 3, p e1003500 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2954212","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3967925","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:3967925","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3967925","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003500","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003500","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003500&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1485621585","display_name":null,"funder_award_id":"CCF-1149811","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G2293884288","display_name":"CAREER:  Exact and Approximate Algorithms for 3D Structure Modeling of Protein-Protein Interactions","funder_award_id":"1149811","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G704483839","display_name":null,"funder_award_id":"R01 GM089753","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7060176192","display_name":null,"funder_award_id":"R01GM089753","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"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"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1936662467.pdf","grobid_xml":"https://content.openalex.org/works/W1936662467.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1540530720","https://openalex.org/W1590648220","https://openalex.org/W1936662467","https://openalex.org/W1967538863","https://openalex.org/W1969153299","https://openalex.org/W1969752145","https://openalex.org/W1973714307","https://openalex.org/W2005647400","https://openalex.org/W2020816856","https://openalex.org/W2029460515","https://openalex.org/W2051210555","https://openalex.org/W2053069893","https://openalex.org/W2057447180","https://openalex.org/W2057624533","https://openalex.org/W2058336694","https://openalex.org/W2060809301","https://openalex.org/W2062018285","https://openalex.org/W2062693912","https://openalex.org/W2068886104","https://openalex.org/W2080336769","https://openalex.org/W2085277871","https://openalex.org/W2088761464","https://openalex.org/W2090617952","https://openalex.org/W2093615982","https://openalex.org/W2099075703","https://openalex.org/W2102124048","https://openalex.org/W2102245393","https://openalex.org/W2117486996","https://openalex.org/W2124158580","https://openalex.org/W2126131681","https://openalex.org/W2129913453","https://openalex.org/W2138122982","https://openalex.org/W2140244239","https://openalex.org/W2145268834","https://openalex.org/W2145358391","https://openalex.org/W2147145103","https://openalex.org/W2147667050","https://openalex.org/W2149521267","https://openalex.org/W2149531726","https://openalex.org/W2156899368","https://openalex.org/W2158714788","https://openalex.org/W2164278908","https://openalex.org/W2164652663","https://openalex.org/W2166701319","https://openalex.org/W2170960297","https://openalex.org/W4247074653","https://openalex.org/W4292363360","https://openalex.org/W6601946118","https://openalex.org/W6959871885"],"related_works":["https://openalex.org/W1482324242","https://openalex.org/W2051969447","https://openalex.org/W2187357871","https://openalex.org/W1989090710","https://openalex.org/W1741740882","https://openalex.org/W24291664","https://openalex.org/W2005647400","https://openalex.org/W2804480386","https://openalex.org/W65850283","https://openalex.org/W3186624150"],"abstract_inverted_index":{"Sequence-based":[0],"protein":[1,20,36,90,144],"homology":[2,72,151,182,204,260],"detection":[3,73,152,183],"has":[4],"been":[5],"extensively":[6],"studied":[7],"and":[8,56,101,133,180,184,207,212,220,223,237,243],"so":[9],"far":[10],"the":[11,138,198,277,280],"most":[12],"sensitive":[13,157],"method":[14,74],"is":[15,41,62,264],"based":[16],"upon":[17],"comparison":[18,61,148],"of":[19,31,77,88,98,109,142,176,214,225,239,272,279],"sequence":[21,28,32,39],"profiles,":[22],"which":[23],"are":[24,255],"derived":[25],"from":[26],"multiple":[27],"alignment":[29,178],"(MSA)":[30],"homologs":[33],"in":[34,174,276],"a":[35,45,70,82,89,93,143],"family.":[37,145],"A":[38,270],"profile":[40],"usually":[42],"represented":[43],"as":[44],"position-specific":[46],"scoring":[47,94],"matrix":[48],"(PSSM)":[49],"or":[50,59,160,171],"an":[51,103],"HMM":[52,117,170],"(Hidden":[53],"Markov":[54,83],"Model)":[55],"accordingly":[57],"PSSM-PSSM":[58,161,206],"HMM-HMM":[60,159,208],"used":[63],"for":[64,137,149,190,203,258,266],"homolog":[65],"detection.":[66,261],"This":[67,247],"paper":[68,274],"presents":[69],"new":[71],"MRFalign,":[75],"consisting":[76],"three":[78],"key":[79],"components:":[80],"1)":[81],"Random":[84],"Fields":[85],"(MRF)":[86],"representation":[87],"family;":[91],"2)":[92],"function":[95],"measuring":[96],"similarity":[97],"two":[99,113],"MRFs;":[100],"3)":[102],"efficient":[104],"ADMM":[105],"(Alternating":[106],"Direction":[107],"Method":[108],"Multipliers)":[110],"algorithm":[111],"aligning":[112],"MRFs.":[114],"Compared":[115],"to":[116],"that":[118,165,185,250],"can":[119,127],"only":[120],"model":[121,128],"very":[122,256],"short-range":[123],"residue":[124,130,252],"correlation,":[125],"MRFs":[126],"long-range":[129,251],"interaction":[131,253],"pattern":[132],"thus,":[134],"encode":[135],"information":[136],"global":[139],"3D":[140],"structure":[141],"Consequently,":[146],"MRF-MRF":[147],"remote":[150,181],"shall":[153],"be":[154],"much":[155],"more":[156],"than":[158],"comparison.":[162],"Experiments":[163],"confirm":[164],"MRFalign":[166,186,233],"outperforms":[167],"several":[168],"popular":[169],"PSSM-based":[172],"methods":[173],"terms":[175],"both":[177],"accuracy":[179],"works":[187],"particularly":[188],"well":[189],"mainly":[191],"beta":[192],"proteins.":[193],"For":[194],"example,":[195],"tested":[196],"on":[197,210,221,235],"benchmark":[199],"SCOP40":[200],"(8353":[201],"proteins)":[202],"detection,":[205],"succeed":[209],"48%":[211],"52%":[213],"proteins,":[215,226],"respectively,":[216,227],"at":[217,228,241,268],"superfamily":[218,242],"level,":[219,245],"15%":[222],"27%":[224],"fold":[229,244],"level.":[230],"In":[231],"contrast,":[232],"succeeds":[234],"57.3%":[236],"42.5%":[238],"proteins":[240],"respectively.":[246],"study":[248],"implies":[249],"patterns":[254],"helpful":[257],"sequence-based":[259],"The":[262],"software":[263],"available":[265],"download":[267],"http://raptorx.uchicago.edu/download/.":[269],"summary":[271],"this":[273],"appears":[275],"proceedings":[278],"RECOMB":[281],"2014":[282],"conference,":[283],"April":[284],"2-5.":[285]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}