{"id":"https://openalex.org/W2007688939","doi":"https://doi.org/10.1186/1471-2105-9-436","title":"Prediction of TF target sites based on atomistic models of protein-DNA complexes","display_name":"Prediction of TF target sites based on atomistic models of protein-DNA complexes","publication_year":2008,"publication_date":"2008-10-16","ids":{"openalex":"https://openalex.org/W2007688939","doi":"https://doi.org/10.1186/1471-2105-9-436","mag":"2007688939","pmid":"https://pubmed.ncbi.nlm.nih.gov/18922190"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-436","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-436","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-436","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/10.1186/1471-2105-9-436","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081867406","display_name":"Vladimir Espinosa Angarica","orcid":"https://orcid.org/0000-0002-3268-8730"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Vladimir Espinosa Angarica","raw_affiliation_strings":["Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Espa\u00f1a. vespinosa@gmail.com","Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Espa\u00f1a"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Espa\u00f1a. vespinosa@gmail.com","institution_ids":["https://openalex.org/I255234318"]},{"raw_affiliation_string":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Espa\u00f1a","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074784061","display_name":"Abel Gonz\u00e1lez-P\u00e9rez","orcid":"https://orcid.org/0000-0002-8582-4660"},"institutions":[{"id":"https://openalex.org/I4210132269","display_name":"Centro Nacional de Investigaciones Cient\u00edficas","ror":"https://ror.org/03zxtdc90","country_code":"CU","type":"facility","lineage":["https://openalex.org/I4210132269"]}],"countries":["CU"],"is_corresponding":false,"raw_author_name":"Abel Gonz\u00e1lez P\u00e9rez","raw_affiliation_strings":["Centro Nacional de Bioinform\u00e1tica, Industria y San Jos\u00e9, Capitolio Nacional, CP 10200, Habana Vieja, Ciudad de la Habana, Cuba"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de Bioinform\u00e1tica, Industria y San Jos\u00e9, Capitolio Nacional, CP 10200, Habana Vieja, Ciudad de la Habana, Cuba","institution_ids":["https://openalex.org/I4210132269"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000425403","display_name":"Ana Tereza Ribeiro de Vasconcelos","orcid":"https://orcid.org/0000-0002-4632-2086"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ana T Vasconcelos","raw_affiliation_strings":["Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica, Av. Getulio Vargas 333, Quitandinha, CEP 25651-075, Petr\u00f3polis, Rio de Janeiro, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica, Av. Getulio Vargas 333, Quitandinha, CEP 25651-075, Petr\u00f3polis, Rio de Janeiro, Brasil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079232768","display_name":"Julio Collado\u2010Vides","orcid":"https://orcid.org/0000-0001-8780-7664"},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Julio Collado-Vides","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av. Universidad s/n., Colonia Chamilpa, 62210, Cuernavaca, Morelos, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av. Universidad s/n., Colonia Chamilpa, 62210, Cuernavaca, Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091306558","display_name":"Bruno Contreras\u2010Moreira","orcid":"https://orcid.org/0000-0002-5462-907X"},"institutions":[{"id":"https://openalex.org/I4210085944","display_name":"Fundacion Agencia Aragonesa para la Investigacion y el Desarrollo","ror":"https://ror.org/007bpwb04","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210085944"]},{"id":"https://openalex.org/I4210143242","display_name":"Estaci\u00f3n Experimental de Aula Dei","ror":"https://ror.org/056a37x91","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210143242"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["ES","MX"],"is_corresponding":false,"raw_author_name":"Bruno Contreras-Moreira","raw_affiliation_strings":["Fundaci\u00f3n ARAID, Paseo Mar\u00eda Agust\u00edn 36, Zaragoza, Espa\u00f1a","Laboratory of Computational Biology, Estaci\u00f3n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient\u00edficas, Av. Monta\u00f1ana 1.005, 50059, Zaragoza, Espa\u00f1a","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av. Universidad s/n., Colonia Chamilpa, 62210, Cuernavaca, Morelos, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n ARAID, Paseo Mar\u00eda Agust\u00edn 36, Zaragoza, Espa\u00f1a","institution_ids":["https://openalex.org/I4210085944"]},{"raw_affiliation_string":"Laboratory of Computational Biology, Estaci\u00f3n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient\u00edficas, Av. Monta\u00f1ana 1.005, 50059, Zaragoza, Espa\u00f1a","institution_ids":["https://openalex.org/I4210143242"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av. Universidad s/n., Colonia Chamilpa, 62210, Cuernavaca, Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5081867406"],"corresponding_institution_ids":["https://openalex.org/I255234318"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.8196,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.84148765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"436","last_page":"436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8977000117301941,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8977000117301941,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.042100001126527786,"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":0.013299999758601189,"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/computational-biology","display_name":"Computational biology","score":0.7163166403770447},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5465712547302246},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5431197881698608},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5004382133483887},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.47132614254951477},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45119142532348633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4443114101886749},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4378418028354645},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.43700048327445984},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37215888500213623},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3649362623691559},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35598456859588623},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3015329837799072},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1775345802307129}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7163166403770447},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5465712547302246},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5431197881698608},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5004382133483887},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.47132614254951477},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45119142532348633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4443114101886749},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4378418028354645},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.43700048327445984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37215888500213623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3649362623691559},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35598456859588623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3015329837799072},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1775345802307129},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"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":"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","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":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-9-436","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-436","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-436","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:18922190","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18922190","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:digital.csic.es:10261/8952","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/8952","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:doaj.org/article:1e3dbf165bb5486e840330861feaefbb","is_oa":true,"landing_page_url":"https://doaj.org/article/1e3dbf165bb5486e840330861feaefbb","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":"BMC Bioinformatics, Vol 9, Iss 1, p 436 (2008)","raw_type":"article"},{"id":"pmh:oai:orbilu.uni.lu:10993/16681","is_oa":false,"landing_page_url":"https://orbilu.uni.lu/handle/10993/16681","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 9, 436 (2008)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:pubmedcentral.nih.gov:2585596","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2585596","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-436","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-436","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-436","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":[],"awards":[{"id":"https://openalex.org/G5143671052","display_name":null,"funder_award_id":"R01-GM071962","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7353960246","display_name":null,"funder_award_id":"R01 GM071962","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320312331","display_name":"Banco Santander","ror":"https://ror.org/017d1hs72"},{"id":"https://openalex.org/F4320323401","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25"},{"id":"https://openalex.org/F4320324111","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28"},{"id":"https://openalex.org/F4320325124","display_name":"CYTED Ciencia y Tecnolog\u00eda para el Desarrollo","ror":"https://ror.org/03myqtf56"},{"id":"https://openalex.org/F4320329058","display_name":"Fundaci\u00f3n Carolina","ror":"https://ror.org/028c4z094"},{"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2007688939.pdf","grobid_xml":"https://content.openalex.org/works/W2007688939.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1562374859","https://openalex.org/W1644724366","https://openalex.org/W1973382304","https://openalex.org/W1974901186","https://openalex.org/W1977312774","https://openalex.org/W1980722147","https://openalex.org/W1983703472","https://openalex.org/W1992812238","https://openalex.org/W1999755087","https://openalex.org/W2003967338","https://openalex.org/W2013238066","https://openalex.org/W2018507982","https://openalex.org/W2026979173","https://openalex.org/W2028834893","https://openalex.org/W2037099334","https://openalex.org/W2042303986","https://openalex.org/W2048241051","https://openalex.org/W2051628563","https://openalex.org/W2054823707","https://openalex.org/W2055228856","https://openalex.org/W2061307445","https://openalex.org/W2063006759","https://openalex.org/W2063735856","https://openalex.org/W2070871842","https://openalex.org/W2072547387","https://openalex.org/W2072920810","https://openalex.org/W2074645168","https://openalex.org/W2074703985","https://openalex.org/W2077496082","https://openalex.org/W2082835279","https://openalex.org/W2085277871","https://openalex.org/W2090250026","https://openalex.org/W2095150400","https://openalex.org/W2095994064","https://openalex.org/W2097396311","https://openalex.org/W2098089372","https://openalex.org/W2098134392","https://openalex.org/W2108765440","https://openalex.org/W2109872885","https://openalex.org/W2110281506","https://openalex.org/W2112110885","https://openalex.org/W2116109811","https://openalex.org/W2119804413","https://openalex.org/W2120651379","https://openalex.org/W2127057035","https://openalex.org/W2135486368","https://openalex.org/W2137154596","https://openalex.org/W2145218186","https://openalex.org/W2149769193","https://openalex.org/W2150293502","https://openalex.org/W2155601193","https://openalex.org/W2158266834","https://openalex.org/W2161276847","https://openalex.org/W2161652323","https://openalex.org/W2169837652","https://openalex.org/W4252178616"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237","https://openalex.org/W2990314835","https://openalex.org/W2131319730","https://openalex.org/W3130075881"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,203],"specific":[2,43],"recognition":[3,44],"of":[4,19,49,52,81,95,115,124,148],"genomic":[5],"cis-regulatory":[6],"elements":[7],"by":[8],"transcription":[9],"factors":[10],"(TFs)":[11],"plays":[12],"an":[13,34,98],"essential":[14],"role":[15],"in":[16,29,62],"the":[17,24,47,59,79,90,107,113,121,137,154,157,174,183],"regulation":[18],"coordinated":[20],"gene":[21],"expression.":[22],"Studying":[23],"mechanisms":[25],"determining":[26],"binding":[27,122,201],"specificity":[28],"protein-DNA":[30,218],"interactions":[31],"is":[32,103,139,159,208],"thus":[33],"important":[35],"goal.":[36],"Most":[37],"current":[38],"approaches":[39],"for":[40,73,173,182],"modeling":[41],"TF":[42,200],"rely":[45],"on":[46,167],"knowledge":[48],"large":[50],"sets":[51],"cognate":[53],"target":[54],"sites":[55],"and":[56,92,127,177,210],"consider":[57],"only":[58],"information":[60,88,193],"contained":[61],"their":[63],"primary":[64],"sequence.":[65],"RESULTS:":[66],"Here":[67],"we":[68],"describe":[69],"a":[70,82,162],"structure-based":[71],"methodology":[72],"predicting":[74],"sequence":[75,180],"motifs":[76,181],"starting":[77],"from":[78],"coordinates":[80],"TF-DNA":[83],"complex.":[84],"Our":[85,187],"algorithm":[86,158],"combines":[87],"regarding":[89],"direct":[91],"indirect":[93],"readout":[94],"DNA":[96],"into":[97],"atomistic":[99],"statistical":[100],"model,":[101],"which":[102],"used":[104,197],"to":[105,118,132,141,198,214],"estimate":[106,120],"interaction":[108],"potential.":[109],"We":[110],"first":[111],"measure":[112],"ability":[114],"our":[116],"method":[117,138,165,205],"correctly":[119],"specificities":[123],"eight":[125],"prokaryotic":[126],"eukaryotic":[128],"TFs":[129],"that":[130,146,190],"belong":[131],"different":[133],"structural":[134,164,192],"superfamilies.":[135],"Secondly,":[136],"applied":[140,213],"two":[142],"homology":[143,184],"models,":[144],"finding":[145],"sampling":[147],"interface":[149],"side-chain":[150],"rotamers":[151],"remarkably":[152],"improves":[153],"results.":[155],"Thirdly,":[156],"compared":[160],"with":[161],"reference":[163],"based":[166],"contact":[168],"counts,":[169],"obtaining":[170],"comparable":[171],"predictions":[172],"experimental":[175],"complexes":[176],"more":[178],"accurate":[179],"models.":[185],"CONCLUSION:":[186],"results":[188],"demonstrate":[189],"atomic-detail":[191],"can":[194],"be":[195,212],"feasibly":[196],"predict":[199],"sites.":[202],"computational":[204],"presented":[206],"here":[207],"universal":[209],"might":[211],"other":[215],"systems":[216],"involving":[217],"recognition.":[219]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
