Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.

ABSTRACT:

Background

Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated.

Methods

In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against

SUBMITTER: Feinstein WP 

PROVIDER: S-EPMC4468813 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature