Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 55, Issue 4, Pages 885-894Publisher
WILEY
DOI: 10.1002/prot.20111
Keywords
protein function prediction; three-dimensional structure; Connolly surface; Poisson-Boltzmann equation; statistical potential; computational method; protein informatics
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Protein-DNA interactions play an essential role in the genetic activities of life. Many structures of protein-DNA complexes are already known, but the common rules on how and where proteins bind to DNA have not emerged. Many attempts have been made to predict protein-DNA interactions using structural information, but the success rate is still about 80%. We analyzed 63 protein-DNA complexes by focusing our attention on the shape of the molecular surface of the protein and DNA, along with the electrostatic potential on the surface, and constructed a new statistical evaluation function to make predictions of DNA interaction sites on protein molecular surfaces. The shape of the molecular surface was described by a combination of local and global average curvature, which are intended to describe the small convex and concave and the large-scale concave curvatures of the protein surface preferentially appearing at DNA-binding sites. Using these structural features, along with the electrostatic potential obtained by solving the Poisson-Boltzmann equation numerically, we have developed prediction schemes with 86% and 96% accuracy for DNA-binding and non-DNA-binding proteins, respectively. (C) 2004 Wiley-Liss, Inc.
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