Journal of Data Mining in Genomics & Proteomics

Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain

Publications

• Commentary   
  Short Commentary on: On the Prediction of DNA-binding Preferences of C2H2-ZF Domains Using Structural Models: Application on Human CTCF
  Author(s): Alberto Meseguer, Ruben Molina-Fernández, Narcis Fernandez-Fuentes, Oriol Fornes* and Baldo Oliva*
  
  In the work entitled “On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF” we present a new computational method to predict the DNA-binding preferences for Cis2-His2 zinc finger (C2H2-ZF) protein-domains from their amino acid sequence or structure. The method uses the structures of protein-DNA complexes to calculate a set of knowledge-based statistical potentials. Given the low numbers of protein-DNA complexes with known structure, we supplement the set of structures with experimental yeast-one-hybrid interactions of more than 170000 sequence-designed C2H2-ZF domains. We have implemented a server to model the structure of any protein-DNA complex of this family and derive its theoretical Position Weight Matrix based on the best scores of interactions calculated with the statistical potential.. View more»
  

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