Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.

ABSTRACT: DNA-binding proteins (DBPs) participate in various crucial processes in the life-cycle of the cells, and the identification and characterization of these proteins is of great importance. We present here a random forests classifier for identifying DBPs among proteins with known 3D structures. First, clusters of evolutionarily conserved regions (patches) on the surface of proteins were detected using the PatchFinder algorithm; earlier studies showed that these regions are typically the functionally important regions of proteins. Next, we trained a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein, including its dipole moment. Using 10-fold cros

SUBMITTER: Nimrod G 

PROVIDER: S-EPMC2726711 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature