Publication Date:
2012-08-23
Description:
We present a set of four parameters that in combination can predict DNA-binding residues on protein structures to a high degree of accuracy. These are the number of evolutionary conserved residues ( N cons ) and their spatial clustering ( e ), hydrogen bond donor capability ( D p ) and residue propensity ( R p ). We first used these parameters to characterize 130 interfaces in a set of 126 DNA-binding proteins (DBPs). The applicability of these parameters both individually and in combination, to distinguish the true binding region from the rest of the protein surface was then analyzed. R p shows the best performance identifying the true interface with the top rank in 83% cases. Importantly, we also used the unbound-bound test cases of the protein–DNA docking benchmark to test the efficacy of our method. When applied to the unbound form of the DBP s, R p can distinguish 86% cases. Finally, we have applied the SVM approach for recognizing the interface region using the above parameters along with the individual amino acid composition as attributes. The accuracy of prediction is 90.5% for the bound structures and 93.6% for the unbound form of the proteins.
Keywords:
Protein-nucleic acid interaction, Computational Methods
Print ISSN:
0305-1048
Electronic ISSN:
1362-4962
Topics:
Biology
