English   español  
Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/17059
Compartir / Impacto:
Título : 3D-footprint: a database for the structural analysis of protein–DNA complexes
Autor : Contreras-Moreira, Bruno
Palabras clave : protein-DNA
interface
specificity
database
Fecha de publicación : 2010
Citación : Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein–DNA complexes. Nucleic Acids Research 38: D91-D97 (2010)
Resumen: 3D-footprint is a living database, updated and curated on a weekly basis, which provides estimates of binding specificity for all protein–DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Each complex in the database is dissected to draw interface graphs and footprint logos, and two complementary algorithms are employed to characterize binding specificity. Moreover, oligonucleotide sequences extracted from literature abstracts are reported in order to show the range of variant sites bound by each protein and other related proteins. Benchmark experiments, including comparisons with expert-curated databases RegulonDB and TRANSFAC, support the quality of structure-based estimates of specificity. The relevant content of the database is available for download as flat files and it is also possible to use the 3D-footprint pipeline to analyze protein coordinates input by the user. 3D-footprint is available at http://floresta.eead.csic.es/3dfootprint with demo buttons and a comprehensive tutorial that illustrates the main uses of this resource.
Versión del editor: http://dx.doi.org/10.1093/nar/gkp781
URI : http://hdl.handle.net/10261/17059
DOI: 10.1093/nar/gkp781
ISSN: 0305-1048 (Print)
1362-4962 (Online)
Aparece en las colecciones: (EEAD) Artículos
Ficheros en este ítem:
Fichero Descripción Tamaño Formato  
3Dfootprint2009.pdf457,05 kBAdobe PDFVista previa
Visualizar/Abrir
Mostrar el registro completo
 



NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.