PocketPicker: analysis of ligand binding-sites with shape descriptors.

ABSTRACT:

Background

Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design. Characterizing the active site's shape as well as the distribution of surrounding residues plays an important role for a variety of applications such as automated ligand docking or in situ modeling. Comparing the shape similarity of binding site geometries of related proteins provides further insights into the mechanisms of ligand binding.

Results

We present PocketPicker, an automated grid-based technique for the prediction of protein binding pockets that specifies the shape of a potential binding-site with regard to its buriedness. The method was applied to a representative set of protein-ligand complexes and their corresponding

SUBMITTER: Weisel M 

PROVIDER: S-EPMC1994066 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature