English   español  
Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/8952
Compartir / Impacto:
Estadísticas
Add this article to your Mendeley library MendeleyBASE
Citado 32 veces en Web of Knowledge®  |  Pub MebCentral Ver citas en PubMed Central  |  Ver citas en Google académico
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL
Exportar otros formatos: Exportar EndNote (RIS)Exportar bibText (RIS)Exportar csv (RIS)
Título

Prediction of TF target sites based on atomistic models of protein-DNA complexes

Autor Espinosa Angarica, Vladimir; Pérez, A.G.; Vasconcelos, A.T.; Collado-Vides, Julio; Contreras-Moreira, Bruno
Palabras clave protein-DNA complex
prediction
transcription factor site
atomistic model
Fecha de publicación 2-dic-2008
Citación BMC Bioinformatics 9: 436 (2008)
ResumenBackground The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.
Versión del editorhttp://www.biomedcentral.com/1471-2105/9/436
URI http://hdl.handle.net/10261/8952
DOI10.1186/1471-2105-9-436
Aparece en las colecciones: (EEAD) Artículos
Ficheros en este ítem:
Fichero Descripción Tamaño Formato  
1471-2105-9-436.pdf702,83 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.