DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

ABSTRACT: Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of DNA-targeting proteins. Characteristics of such binding sites may form the basis for predicting DNA-binding sites from the structures of proteins alone. Such an approach has been successfully developed for predicting protein-protein interface. Here this approach is adapted for predicting DNA-binding sites. We used a representative set of 264 protein-DNA complexes from the Protein Data Bank to analyze characteristics and to train and test a neural network predictor of DNA-binding sites. The input to the predictor consisted of PSI-blast sequence profiles and solvent accessibilities of each surface residue and 14 of its closest neighboring residues. Predicted DNA-contacting resid

SUBMITTER: Tjong H 

PROVIDER: S-EPMC1865077 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature