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Título: | Comparative footprinting of DNA-binding proteins |
Autor: | Contreras-Moreira, Bruno CSIC ORCID ; Collado-Vides, Julio | Palabras clave: | Protein Sequence Homology Sequence analysis Protein footprinting Protein binding Escherichia coli Binding sites Computer simulation DNA-Binding Proteins |
Fecha de publicación: | 2006 | Editor: | Oxford University Press | Citación: | Bioinformatics 22 (14): E74- E80 (2006) | Resumen: | Motivation: Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and bio-technology. Traditionally it has been applied to model the structure of proteins on their own or bound to small ligands, although more recently it has also been used to model protein-protein interfaces. This work is the first to systematically analyze whether comparative models of protein-DNA complexes could be built and be useful for predicting DNA binding sites. Results: First, we describe the structural and evolutionary conservation of protein-DNA interfaces, and the limits they impose on modelling accuracy. Second, we find that side-chains from contacting residues can be reasonably modeled and therefore used to identify contacting nucleotides. Third, the DNASITE protocol is implemented and different parameters are benchmarked on a set of 85 regulators from Escherichia coli. Results show that comparative foot-printing can make useful predictions based solely on structural data, depending primarily on the interface identity with respect to the template used. | Descripción: | 7 Pág., 4 Fig., 2 Tabl. The original version is available at: http://bioinformatics.oxfordjournals.org/content/22/14/e74 | Versión del editor: | http://dx.doi.org/10.1093/bioinformatics/btl215 | URI: | http://hdl.handle.net/10261/98567 | DOI: | 10.1093/bioinformatics/btl215 | Identificadores: | doi: 10.1093/bioinformatics/btl215 issn: 1367-4803 |
Aparece en las colecciones: | (EEAD) Artículos |
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ContrerasB_Bioinformatics_2006_22_14.pdf | 833,16 kB | Adobe PDF | Visualizar/Abrir |
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