PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

ABSTRACT: Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSu

SUBMITTER: Hu B 

PROVIDER: S-EPMC4200761 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature