Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

ABSTRACT: Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemi

SUBMITTER: Sael L 

PROVIDER: S-EPMC3294165 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature