PharmDock: a pharmacophore-based docking program.

ABSTRACT:

Background

Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and ranking based on optimized protein-based pharmacophore models with local optimization using an empirical scoring function.

Results

Tests of PharmDock on ligand pose prediction, binding affinity estimation, compound ranking and virtual screening yielded comparable or better performance to existing and widely used docking programs. The docking program comes with an easy-to-use GUI within

SUBMITTER: Hu B 

PROVIDER: S-EPMC4012150 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature