Dock odysseys. II. The evaluation of AutoDock program and its comparison with other docking programs


Zengjian Hu1, Shaomeng Wang2, and William M. Southerland1. (1) Department of Biochemistry and Molecular Biology, Howard University College of Medicine and the Howard University Drug Discovery Unit, 520 West Street, Northwest, Room 324, Washington, DC 20059, (2) Intel Med, The University of Michigan, 1500 E. Medical Center Dr, Ann Arbor, MI 48105
In recent years, computational high-throughput docking (HTD) has emerged as a very powerful tool for identifying novel lead compounds. In principle, HTD should discover all of the ligands of interest in a database, but in practice, HTD suffers from false positives and false negatives. In this study, we evaluated the AutoDock program for its quality and accuracy in identifying and predicting ligand binding modes. AutoDock is one of the most widely used docking programs in computational binding studies. Our results show that AutoDock is able to predict preotein-ligand complex structures with reasonable accuracy and speed. We also compared AutoDock program with three other popular used programs, DOCK, FlexX and GOLD. We found its performance batter than these three programs. Its use in HTD should enhance efficiency in the discovery of lead compounds (* This work is supported in part by grant RCMI-NIH 2G12RR03048).

8:00 PM-10:00 PM, Monday, August 23, 2004 Pennsylvania Convention Center -- Hall D, Sci-Mix

Division of Chemical Information

The 228th ACS National Meeting, in Philadelphia, PA, August 22-26, 2004