Virtual Screening Using Pharmacophore Models Retrieved from Molecular Dynamic Simulations.

ABSTRACT: Pharmacophore models are widely used for the identification of promising primary hits in compound large libraries. Recent studies have demonstrated that pharmacophores retrieved from protein-ligand molecular dynamic trajectories outperform pharmacophores retrieved from a single crystal complex structure. However, the number of retrieved pharmacophores can be enormous, thus, making it computationally inefficient to use all of them for virtual screening. In this study, we proposed selection of distinct representative pharmacophores by the removal of pharmacophores with identical three-dimensional (3D) pharmacophore hashes. We also proposed a new conformer coverage approach in order to rank compounds using all representative pharmacophores. Our results for four cyclin-dependent kinase 2 (CDK2

SUBMITTER: Polishchuk P 

PROVIDER: S-EPMC6929024 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature