Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters.

ABSTRACT: 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 (ρ(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 o

SUBMITTER: Dey S 

PROVIDER: S-EPMC3424558 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature