Prediction of DNA-binding residues from sequence
1Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, 2Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St Nicholas Ave. Rm. 802, 3D.E.Shaw Research, 120 West Forty Fifth Street (current affiliation) and 4NorthEast Structural Genomics Consortium (NESG), Columbia University, 1130 St Nicholas Ave. Rm. 802, New York, NY 10032, USA
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Thousands of proteins are known to bind to DNA; for most of them the mechanism of action and the residues that bind to DNA, i.e. the binding sites, are yet unknown. Experimental identification of binding sites requires expensive and laborious methods such as mutagenesis and binding essays. Hence, such studies are not applicable on a large scale. If the 3D structure of a protein is known, it is often possible to predict DNA-binding sites in silico. However, for most proteins, such knowledge is not available.
Results: It has been shown that DNA-binding residues have distinct biophysical characteristics. Here we demonstrate that these characteristics are so distinct that they enable accurate prediction of the residues that bind DNA directly from amino acid sequence, without requiring any additional experimental or structural information. In a cross-validation based on the largest non-redundant dataset of high-resolution protein–DNA complexes available today, we found that 89% of our predictions are confirmed by experimental data. Thus, it is now possible to identify DNA-binding sites on a proteomic scale even in the absence of any experimental data or 3D-structural information.
Availability: http://cubic.bioc.columbia.edu/services/disis
Contact: yo135{at}columbia.edu
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