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Journal of Computer-Aided Molecular Design 17: 755763, 2003. 2004 Kluwer Academic Publishers. Printed in the Netherlands.

Summary: Journal of Computer-Aided Molecular Design 17: 755­763, 2003.
© 2004 Kluwer Academic Publishers. Printed in the Netherlands.
Comparative study of several algorithms for flexible ligand docking
Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan & Charles L. Brooks III
Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road,
La Jolla, CA 92037, USA
Received 1 August 2003; accepted in revised form 12 November 2003
Key words: AutoDock, DOCK, FlexX, Gold, ICM
We have performed a comparative assessment of several programs for flexible molecular docking: DOCK
4.0, FlexX 1.8, AutoDock 3.0, GOLD 1.2 and ICM 2.8. This was accomplished using two different studies:
docking experiments on a data set of 37 protein­ligand complexes and screening a library containing 10,037 entries
against 11 different proteins. The docking accuracy of the methods was judged based on the corresponding rank-
one solutions. We have found that the fraction of molecules docked with acceptable accuracy is 0.47, 0.31, 0.35,
0.52 and 0.93 for, respectively, AutoDock, DOCK, FlexX, GOLD and ICM. Thus ICM provided the highest
accuracy in ligand docking against these receptors. The results from the other programs are found to be less
accurate and of approximately the same quality. A speed comparison demonstrated that FlexX was the fastest
and AutoDock was the slowest among the tested docking programs. The database screening was performed using
DOCK, FlexX and ICM. ICM was able to identify the original ligands within the top 1% of the total library in


Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego


Collections: Biology and Medicine