From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.

ABSTRACT: DNA-protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA-protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA-protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA-protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DN

SUBMITTER: Gao M 

PROVIDER: S-EPMC2659451 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature