{"id":"https://openalex.org/W2135486368","doi":"https://doi.org/10.1093/bioinformatics/btm148","title":"TFmodeller: comparative modelling of protein\u2013DNA complexes","display_name":"TFmodeller: comparative modelling of protein\u2013DNA complexes","publication_year":2007,"publication_date":"2007-04-25","ids":{"openalex":"https://openalex.org/W2135486368","doi":"https://doi.org/10.1093/bioinformatics/btm148","mag":"2135486368","pmid":"https://pubmed.ncbi.nlm.nih.gov/17459960"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm148","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btm148","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091306558","display_name":"Bruno Contreras\u2010Moreira","orcid":"https://orcid.org/0000-0002-5462-907X"},"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":true,"raw_author_name":"Bruno Contreras-Moreira","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av.Universidad, s/n, 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, 62210 Cuernavaca, Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015711669","display_name":"Pierre-Alain Branger","orcid":null},"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":"Pierre-Alain Branger","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Av.Universidad, s/n, 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, 62210 Cuernavaca, Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"last","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, 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, 62210 Cuernavaca, Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091306558"],"corresponding_institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0659,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.76123908,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"13","first_page":"1694","last_page":"1696"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6592000126838684,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6592000126838684,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.04450000077486038,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.03579999879002571,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/schematic","display_name":"Schematic","score":0.6303098797798157},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5566163659095764},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5359694957733154},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.49705079197883606},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.47264593839645386},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4661940634250641},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.46023061871528625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3371841311454773},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2914464473724365},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19358617067337036},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17903956770896912},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14939197897911072}],"concepts":[{"id":"https://openalex.org/C192328126","wikidata":"https://www.wikidata.org/wiki/Q4514647","display_name":"Schematic","level":2,"score":0.6303098797798157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5566163659095764},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5359694957733154},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.49705079197883606},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.47264593839645386},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4661940634250641},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.46023061871528625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3371841311454773},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2914464473724365},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19358617067337036},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17903956770896912},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14939197897911072},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm148","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17459960","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17459960","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm148","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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"}],"funders":[{"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":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1983703472","https://openalex.org/W1996307860","https://openalex.org/W2015403140","https://openalex.org/W2027662098","https://openalex.org/W2070871842","https://openalex.org/W2114520383","https://openalex.org/W2119966574","https://openalex.org/W2126016150","https://openalex.org/W2130479394","https://openalex.org/W2158714788","https://openalex.org/W2161276847","https://openalex.org/W2161732286"],"related_works":["https://openalex.org/W3154683910","https://openalex.org/W1846734616","https://openalex.org/W3134543635","https://openalex.org/W2359532622","https://openalex.org/W2921318524","https://openalex.org/W2377571686","https://openalex.org/W4380988671","https://openalex.org/W1925657225","https://openalex.org/W1649706580","https://openalex.org/W3195608031"],"abstract_inverted_index":{"UNLABELLED:":[0],"Interactions":[1],"between":[2],"proteins":[3],"and":[4,56,72,86,106,113],"DNA":[5],"molecules":[6],"lie":[7],"at":[8,28,123],"the":[9,12,32,44,52,70,82,90],"core":[10],"of":[11,21,35,81,89,95],"fundamental":[13],"cellular":[14],"processes":[15],"such":[16],"as":[17],"transcriptional":[18],"regulation.":[19],"Some":[20],"these":[22],"interactions":[23],"have":[24],"been":[25],"experimentally":[26],"described":[27],"atomic":[29,87],"scale,":[30],"but":[31],"molecular":[33],"details":[34],"many":[36],"others":[37],"remain":[38],"to":[39,59,69],"be":[40],"discovered.":[41],"TFmodeller":[42,99,112],"exploits":[43],"current":[45],"knowledge":[46],"about":[47],"protein-DNA":[48],"interfaces":[49,62],"contained":[50],"in":[51],"Protein":[53],"Data":[54],"Bank":[55],"uses":[57],"it":[58],"model":[60],"similar":[61],"related":[63],"by":[64,98],"homology.":[65],"Results":[66],"are":[67,118],"emailed":[68],"user":[71],"include":[73],"an":[74],"evolutionary":[75],"contact":[76],"matrix,":[77],"a":[78,103],"schematic":[79],"representation":[80],"putative":[83],"binding":[84],"interface":[85,117],"coordinates":[88],"modelled":[91],"complex.":[92],"The":[93],"library":[94],"complexes":[96],"used":[97],"is":[100,107],"updated":[101],"on":[102],"weekly":[104],"basis":[105],"available":[108],"for":[109,120],"download.":[110],"AVAILABILITY:":[111],"its":[114],"web":[115],"service":[116],"free":[119],"academic":[121],"users":[122],"http://www.ccg.unam.mx/tfmodeller.":[124]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
