Paper Info
Title
Galaxydock3: Protein-Ligand Docking That Considers The Full Ligand Conformational Flexibility
Abstract
Predicting conformational changes of both the protein and the ligand is a major challenge when a protein-ligand complex structure is predicted from the unbound protein and ligand structures. Herein, we introduce a new protein-ligand docking program called GalaxyDock3 that considers the full ligand conformational flexibility by explicitly sampling the ligand ring conformation and allowing the relaxation of the full ligand degrees of freedom, including bond angles and lengths. This method is based on the previous version (GalaxyDock2) which performs the global optimization of a designed score function. Ligand ring conformation is sampled from a ring conformation library constructed from structure databases. The GalaxyDock3 score function was trained with an additional bonded energy term for the ligand on a large set of complex structures. The performance of GalaxyDock3 was improved compared to GalaxyDock2 when predicted ligand conformation was used as the input for docking, especially when the input ligand conformation differs significantly from the crystal conformation. GalaxyDock3 also compared favorably with other available docking programs on two benchmark tests that contained diverse ligand rings. The program is freely available at . (c) 2019 Wiley Periodicals, Inc.
Year
DOI
Venue
2019
10.1002/jcc.26050
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
protein-ligand docking, ligand flexibility, ring conformation, global optimization, energy parameter optimization
Global optimization,Ligand,Computational chemistry,Protein–ligand docking,Chemistry
Journal
Volume
Issue
ISSN
40
31
0192-8651
Citations 
PageRank 
References 
0
0.34
0
Authors
3
Name
Order
Citations
PageRank
Jinsol Yang100.68
Minkyung Baek221.38
Chaok Seok316315.89