Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina.

ABSTRACT:

Background

The AutoDock family of software has been widely used in protein-ligand docking research. This study compares AutoDock 4 and AutoDock Vina in the context of virtual screening by using these programs to select compounds active against HIV protease.

Methodology/principal findings

Both programs were used to rank the members of two chemical libraries, each containing experimentally verified binders to HIV protease. In the case of the NCI Diversity Set II, both AutoDock 4 and Vina were able to select active compounds significantly better than random (AUC = 0.69 and 0.68, respectively; p<0.001). The binding energy predictions were highly correlated in this case, with r = 0.63 and iota = 0.82. For a set of larger, more flexible compounds from the Directory of Universal De

SUBMITTER: Chang MW 

PROVIDER: S-EPMC2915912 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature