GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters.
J Comput Chem
; 40(27): 2413-2417, 2019 10 15.
Article
in En
| MEDLINE
| ID: mdl-31173387
ABSTRACT
Protein-protein docking methods are spotlighted for their roles in providing insights into protein-protein interactions in the absence of full structural information by experiment. GalaxyTongDock is an ab initio protein-protein docking web server that performs rigid-body docking just like ZDOCK but with improved energy parameters. The energy parameters were trained by iterative docking and parameter search so that more native-like structures are selected as top rankers. GalaxyTongDock performs asymmetric docking of two different proteins (GalaxyTongDock_A) and symmetric docking of homo-oligomeric proteins with Cn and Dn symmetries (GalaxyTongDock_C and GalaxyTongDock_D). Performance tests on an unbound docking benchmark set for asymmetric docking and a model docking benchmark set for symmetric docking showed that GalaxyTongDock is better or comparable to other state-of-the-art methods. Experimental and/or evolutionary information on binding interfaces can be easily incorporated by using block and interface options. GalaxyTongDock web server is freely available at http//galaxy.seoklab.org/tongdock. © 2019 Wiley Periodicals, Inc.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Quantum Theory
/
Software
/
Proteins
/
Molecular Docking Simulation
Type of study:
Prognostic_studies
Language:
En
Journal:
J Comput Chem
Journal subject:
QUIMICA
Year:
2019
Type:
Article