{"id":"https://openalex.org/W2035202199","doi":"https://doi.org/10.1186/1471-2105-12-83","title":"A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models","display_name":"A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models","publication_year":2011,"publication_date":"2011-03-23","ids":{"openalex":"https://openalex.org/W2035202199","doi":"https://doi.org/10.1186/1471-2105-12-83","mag":"2035202199","pmid":"https://pubmed.ncbi.nlm.nih.gov/21429187"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-83","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-83","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089115213","display_name":"Juliana Bernardes","orcid":"https://orcid.org/0000-0003-1341-4256"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210094040","display_name":"Centro de Tecnologia Mineral","ror":"https://ror.org/00n4vrp79","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210094040","https://openalex.org/I4210151455"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]}],"countries":["BR","FR"],"is_corresponding":true,"raw_author_name":"Juliana S Bernardes","raw_affiliation_strings":["COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. julibinho@gmail.com","UFRJ - Universidade Federal do Rio de Janeiro [Brasil] = Federal University of Rio de Janeiro [Brazil] = Universit\u00e9 f\u00e9d\u00e9rale de Rio de Janeiro [Br\u00e9sil] (Av. Pedro Calmon, 550 - Cidade Universit\u00e1ria, Rio de Janeiro - RJ, 21941-901 - Brazil)","PESC - Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o (Centro de Tecnologia, Bloco H - Sala 319 Caixa Postal: 68511 CEP: 21941-972 Rio de Janeiro, RJ - Brazil)","LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (Biologie Computationnelle et Quantitative UMR 7238 CNRS-Sorbonne-Universit\u00e9, Site des Cordeliers B\u00e2t. A - 4\u00e8me \u00e9tage, 15, Rue de l'Ecole de M\u00e9decine 75006 Paris, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. julibinho@gmail.com","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"UFRJ - Universidade Federal do Rio de Janeiro [Brasil] = Federal University of Rio de Janeiro [Brazil] = Universit\u00e9 f\u00e9d\u00e9rale de Rio de Janeiro [Br\u00e9sil] (Av. Pedro Calmon, 550 - Cidade Universit\u00e1ria, Rio de Janeiro - RJ, 21941-901 - Brazil)","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"PESC - Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o (Centro de Tecnologia, Bloco H - Sala 319 Caixa Postal: 68511 CEP: 21941-972 Rio de Janeiro, RJ - Brazil)","institution_ids":["https://openalex.org/I4210094040"]},{"raw_affiliation_string":"LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (Biologie Computationnelle et Quantitative UMR 7238 CNRS-Sorbonne-Universit\u00e9, Site des Cordeliers B\u00e2t. A - 4\u00e8me \u00e9tage, 15, Rue de l'Ecole de M\u00e9decine 75006 Paris, France - France)","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210097156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038174177","display_name":"Alessandra Carbone","orcid":"https://orcid.org/0000-0003-2098-5743"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4210122170","display_name":"Laboratoire Microorganismes G\u00e9nome et Environnement","ror":"https://ror.org/020ahr442","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I198244214","https://openalex.org/I4210107625","https://openalex.org/I4210122170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alessandra Carbone","raw_affiliation_strings":["CNRS, UMR7238, Laboratoire de G\u00e9nomique des Microorganismes, F-75006, Paris, France","Universit\u00e9 Pierre et Marie Curie, UMR7238, G\u00e9nomique Analytique, 15 rue de l'Ecole de M\u00e9decine, F-75006, Paris, France","LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (Biologie Computationnelle et Quantitative UMR 7238 CNRS-Sorbonne-Universit\u00e9, Site des Cordeliers B\u00e2t. A - 4\u00e8me \u00e9tage, 15, Rue de l'Ecole de M\u00e9decine 75006 Paris, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, UMR7238, Laboratoire de G\u00e9nomique des Microorganismes, F-75006, Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210097156","https://openalex.org/I4210122170"]},{"raw_affiliation_string":"Universit\u00e9 Pierre et Marie Curie, UMR7238, G\u00e9nomique Analytique, 15 rue de l'Ecole de M\u00e9decine, F-75006, Paris, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I4210097156"]},{"raw_affiliation_string":"LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (Biologie Computationnelle et Quantitative UMR 7238 CNRS-Sorbonne-Universit\u00e9, Site des Cordeliers B\u00e2t. A - 4\u00e8me \u00e9tage, 15, Rue de l'Ecole de M\u00e9decine 75006 Paris, France - France)","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210097156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012291023","display_name":"Gerson Zaverucha","orcid":"https://orcid.org/0000-0002-3641-6839"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]},{"id":"https://openalex.org/I4210094040","display_name":"Centro de Tecnologia Mineral","ror":"https://ror.org/00n4vrp79","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210094040","https://openalex.org/I4210151455"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gerson Zaverucha","raw_affiliation_strings":["COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","PESC - Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o (Centro de Tecnologia, Bloco H - Sala 319 Caixa Postal: 68511 CEP: 21941-972 Rio de Janeiro, RJ - Brazil)","UFRJ - Universidade Federal do Rio de Janeiro [Brasil] = Federal University of Rio de Janeiro [Brazil] = Universit\u00e9 f\u00e9d\u00e9rale de Rio de Janeiro [Br\u00e9sil] (Av. Pedro Calmon, 550 - Cidade Universit\u00e1ria, Rio de Janeiro - RJ, 21941-901 - Brazil)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"PESC - Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o (Centro de Tecnologia, Bloco H - Sala 319 Caixa Postal: 68511 CEP: 21941-972 Rio de Janeiro, RJ - Brazil)","institution_ids":["https://openalex.org/I4210094040"]},{"raw_affiliation_string":"UFRJ - Universidade Federal do Rio de Janeiro [Brasil] = Federal University of Rio de Janeiro [Brazil] = Universit\u00e9 f\u00e9d\u00e9rale de Rio de Janeiro [Br\u00e9sil] (Av. Pedro Calmon, 550 - Cidade Universit\u00e1ria, Rio de Janeiro - RJ, 21941-901 - Brazil)","institution_ids":["https://openalex.org/I122140584"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5089115213"],"corresponding_institution_ids":["https://openalex.org/I122140584","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210094040","https://openalex.org/I4210097156"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9733,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.73365321,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"12","issue":"1","first_page":"83","last_page":"83"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.7893999814987183,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.7893999814987183,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.038100000470876694,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.03189999982714653,"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/inductive-logic-programming","display_name":"Inductive logic programming","score":0.7840663194656372},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6240217089653015},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.5595274567604065},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.5556954145431519},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.52912437915802},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45478498935699463},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45076829195022583},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.4504129886627197},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3881475329399109},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3784290552139282},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3367432951927185},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.26691171526908875},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24735960364341736},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16809341311454773},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.165043443441391},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.13197052478790283}],"concepts":[{"id":"https://openalex.org/C2779382394","wikidata":"https://www.wikidata.org/wiki/Q1464197","display_name":"Inductive logic programming","level":2,"score":0.7840663194656372},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6240217089653015},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.5595274567604065},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5556954145431519},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.52912437915802},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45478498935699463},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45076829195022583},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.4504129886627197},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3881475329399109},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3784290552139282},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3367432951927185},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.26691171526908875},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24735960364341736},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16809341311454773},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.165043443441391},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.13197052478790283},{"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":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":"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-12-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-83","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21429187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21429187","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-00684137v1","is_oa":false,"landing_page_url":"https://hal.science/hal-00684137","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2011, 12, pp.83. &#x27E8;10.1186/1471-2105-12-83&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:hal-03911431v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03911431","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2011, 12 (1), pp.83. &#x27E8;10.1186/1471-2105-12-83&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:cd5b3ad30135468f8294b668d0cd6815","is_oa":false,"landing_page_url":"https://doaj.org/article/cd5b3ad30135468f8294b668d0cd6815","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 83 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2087404","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3078102","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-83","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-83","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-83","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.7099999785423279}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322263","display_name":"Conseil R\u00e9gional, \u00cele-de-France","ror":"https://ror.org/04ry1rt27"},{"id":"https://openalex.org/F4320322749","display_name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","ror":"https://ror.org/03kk0s825"},{"id":"https://openalex.org/F4320323678","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Ci\u00eancia e Tecnologia do Estado de Pernambuco","ror":"https://ror.org/02te5rf52"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2035202199.pdf","grobid_xml":"https://content.openalex.org/works/W2035202199.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1486487250","https://openalex.org/W1486662173","https://openalex.org/W1495384623","https://openalex.org/W1497782867","https://openalex.org/W1498433609","https://openalex.org/W1504694836","https://openalex.org/W1966191115","https://openalex.org/W1973714307","https://openalex.org/W1976526581","https://openalex.org/W1987902506","https://openalex.org/W1995918845","https://openalex.org/W2014731953","https://openalex.org/W2045564656","https://openalex.org/W2055043387","https://openalex.org/W2086301041","https://openalex.org/W2097555181","https://openalex.org/W2099075703","https://openalex.org/W2099946731","https://openalex.org/W2104983234","https://openalex.org/W2106882534","https://openalex.org/W2108079689","https://openalex.org/W2117502874","https://openalex.org/W2121950477","https://openalex.org/W2124709175","https://openalex.org/W2125055259","https://openalex.org/W2125725297","https://openalex.org/W2127464112","https://openalex.org/W2128328428","https://openalex.org/W2132573698","https://openalex.org/W2133075481","https://openalex.org/W2137597742","https://openalex.org/W2140141795","https://openalex.org/W2141262207","https://openalex.org/W2141779955","https://openalex.org/W2142013909","https://openalex.org/W2145268834","https://openalex.org/W2145358391","https://openalex.org/W2148279834","https://openalex.org/W2151831732","https://openalex.org/W2153374683","https://openalex.org/W2154218709","https://openalex.org/W2154952425","https://openalex.org/W2158714788","https://openalex.org/W2166559705","https://openalex.org/W2168162717","https://openalex.org/W2169042011","https://openalex.org/W2170421047","https://openalex.org/W2170666908","https://openalex.org/W2170960297","https://openalex.org/W2283504545","https://openalex.org/W2394515930","https://openalex.org/W2490250287","https://openalex.org/W3145289798","https://openalex.org/W4213345021","https://openalex.org/W4252684946","https://openalex.org/W4293249558"],"related_works":["https://openalex.org/W4389116644","https://openalex.org/W2153315159","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W4205463238","https://openalex.org/W2761785940","https://openalex.org/W1482209366","https://openalex.org/W2110523656","https://openalex.org/W2521627374","https://openalex.org/W2035202199"],"abstract_inverted_index":{"BACKGROUND:":[0],"Remote":[1],"homology":[2,183],"detection":[3],"is":[4,178,186],"a":[5,53,152,165,189,199],"hard":[6],"computational":[7,13],"problem.":[8],"Most":[9],"approaches":[10],"have":[11],"trained":[12],"models":[14],"by":[15,115,205],"using":[16,130],"either":[17],"full":[18],"protein":[19,117,166,214],"sequences":[20,47],"or":[21],"multiple":[22],"sequence":[23],"alignments":[24],"(MSA),":[25],"including":[26],"all":[27],"positions.":[28],"However,":[29,148],"when":[30,129],"we":[31,39],"deal":[32],"with":[33],"proteins":[34],"in":[35,74],"the":[36,75,84,108,120,138,141,174,181],"\"twilight":[37],"zone\"":[38],"can":[40,159],"observe":[41],"that":[42,57,126,158,209],"only":[43,173],"some":[44,136],"segments":[45],"of":[46,64,137,140,155,171,194,201,213],"(motifs)":[48,88],"are":[49],"conserved.":[50],"We":[51,106],"introduce":[52],"novel":[54],"logical":[55,156,192],"representation":[56,193],"allows":[58],"us":[59],"to":[60,92,111,146,161],"represent":[61],"physico-chemical":[62,72],"properties":[63],"sequences,":[65],"conserved":[66,71],"amino":[67],"acid":[68],"positions":[69,73],"and":[70,89,100,144,197],"MSA.":[76],"From":[77],"this,":[78],"Inductive":[79],"Logic":[80],"Programming":[81],"(ILP)":[82],"finds":[83],"most":[85,175],"frequent":[86,176,202],"patterns":[87,177],"uses":[90],"them":[91],"train":[93],"propositional":[94],"models,":[95],"such":[96],"as":[97],"decision":[98],"trees":[99],"support":[101],"vector":[102],"machines":[103],"(SVM).":[104],"RESULTS:":[105],"use":[107],"SCOP":[109],"database":[110],"perform":[112],"our":[113,127,149],"experiments":[114],"evaluating":[116],"recognition":[118],"within":[119],"same":[121],"superfamily.":[122],"Our":[123],"results":[124],"show":[125],"methodology":[128],"SVM":[131],"performs":[132],"significantly":[133],"better":[134],"than":[135],"state":[139],"art":[142],"methods,":[143],"comparable":[145],"other.":[147],"method":[150],"provides":[151],"comprehensible":[153],"set":[154,200],"rules":[157],"help":[160],"understand":[162],"what":[163],"determines":[164],"function.":[167],"CONCLUSIONS:":[168],"The":[169],"strategy":[170],"selecting":[172],"effective":[179],"for":[180],"remote":[182],"detection.":[184],"This":[185],"possible":[187],"through":[188,198],"suitable":[190],"first-order":[191],"homologous":[195],"properties,":[196],"patterns,":[203],"found":[204],"an":[206],"ILP":[207],"system,":[208],"summarizes":[210],"essential":[211],"features":[212],"functions.":[215]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
