{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:08:35Z","timestamp":1761894515718},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein\u2013DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download.<\/jats:p>\n               <jats:p>Availability: TFmodeller and its web service interface are free for academic users at http:\/\/www.ccg.unam.mx\/tfmodeller<\/jats:p>\n               <jats:p>Contact: contrera@ccg.unam.mx<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm148","type":"journal-article","created":{"date-parts":[[2007,4,26]],"date-time":"2007-04-26T05:51:25Z","timestamp":1177566685000},"page":"1694-1696","source":"Crossref","is-referenced-by-count":24,"title":["TFmodeller: comparative modelling of protein\u2013DNA complexes"],"prefix":"10.1093","volume":"23","author":[{"given":"Bruno","family":"Contreras-Moreira","sequence":"first","affiliation":[{"name":"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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre-Alain","family":"Branger","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julio","family":"Collado-Vides","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,4,25]]},"reference":[{"key":"2023062708443720100_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023062708443720100_B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023062708443720100_B3","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1110\/ps.03154503","article-title":"A graph-theory algorithm for rapid protein side-chain prediction","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci"},{"key":"2023062708443720100_B4","doi-asserted-by":"crossref","first-page":"E74","DOI":"10.1093\/bioinformatics\/btl215","article-title":"Comparative footprinting of DNA-binding proteins","volume":"22","author":"Contreras-Moreira","year":"2006","journal-title":"Bioinformatics"},{"key":"2023062708443720100_B5","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/S0968-0004(99)01427-9","article-title":"Protein modelling for all","volume":"24","author":"Guex","year":"1999","journal-title":"Trends Biochem Sci"},{"key":"2023062708443720100_B6","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1016\/S0022-2836(02)00571-5","article-title":"Protein\u2013DNA interactions: amino acid conservation and the effects of mutations on binding specificity","volume":"320","author":"Luscombe","year":"2002","journal-title":"J. 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