GalaxyDock2: Protein–ligand docking using beta-complex and global optimization
Article first published online: 23 SEP 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 30, pages 2647–2656, 15 November 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2647–2656. DOI: 10.1002/jcc.23438, , , .
- Issue published online: 10 OCT 2013
- Article first published online: 23 SEP 2013
- Manuscript Accepted: 18 AUG 2013
- Manuscript Revised: 20 JUL 2013
- Manuscript Received: 2 APR 2013
- NRF. Grant Numbers: 2011-0012456, 2011-0030932, 2012M3C1A6035362, 2013R1A2A1A09012229
- NRF. Grant Number: 2012R1A2A1A05026395
- Ministry of Knowledge Economy, Korea. Grant Number: 10040176
- protein–ligand docking;
- Voronoi diagram;
- receptor flexibility;
- conformational space annealing
In this article, an enhanced version of GalaxyDock protein–ligand docking program is introduced. GalaxyDock performs conformational space annealing (CSA) global optimization to find the optimal binding pose of a ligand both in the rigid-receptor mode and the flexible-receptor mode. Binding pose prediction has been improved compared to the earlier version by the efficient generation of high-quality initial conformations for CSA using a predocking method based on a beta-complex derived from the Voronoi diagram of receptor atoms. Binding affinity prediction has also been enhanced by using the optimal combination of energy components, while taking into consideration the energy of the unbound ligand state. The new version has been tested in terms of binding mode prediction, binding affinity prediction, and virtual screening on several benchmark sets, showing improved performance over the previous version and AutoDock, on which the GalaxyDock energy function is based. GalaxyDock2 also performs better than or comparable to other state-of-the-art docking programs. GalaxyDock2 is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html. © 2013 Wiley Periodicals, Inc.