Nucleic Acids Research Advance Access published online on February 6, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm008
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Computational Biology |
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
*To whom correspondence should be addressed. Tel: +1 850 6451336; Fax: +1 850 6447244; Email: zhou{at}sb.fsu.edu
Received August 24, 2006. Revised November 25, 2006. Accepted December 27, 2006.
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 residues cover 60% of actual DNA-contacting residues and have an accuracy of 76%. This method significantly outperforms previous attempts of DNA-binding site predictions. Its application to the prion protein yielded a DNA-binding site that is consistent with recent NMR chemical shift perturbation data, suggesting that it can complement experimental techniques in characterizing protein–DNA interfaces.
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