Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.

ABSTRACT:

Motivation

Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects.

Results

We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-S

SUBMITTER: Zhu X 

PROVIDER: S-EPMC4341070 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature