Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking.

ABSTRACT: Protein-based pharmacophore models derived from protein binding site atoms without the inclusion of any ligand information have become more popular in virtual screening studies. However, the accuracy of protein-based pharmacophore models for reproducing the critical protein-ligand interactions has never been explicitly assessed. In this study, we used known protein-ligand contacts from a large set of experimentally determined protein-ligand complexes to assess the quality of the protein-based pharmacophores in reproducing these critical contacts. We demonstrate how these contacts can be used to optimize the pharmacophore generation procedure to produce pharmacophore models that optimally cover the known protein-ligand interactions. Finally, we explored the potential of the optimized protei

SUBMITTER: Hu B 

PROVIDER: S-EPMC3725268 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature