GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters

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 homooligomeric proteins with C n and D n 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. GalaxyTong Dock web server is freely available at http://galaxy.seoklab.org/ tongdock.

Prediction of protein oligomer structures using GALAXY in CASP13

“…When it failed to detect five templates by sequence‐based search, monomer structure was predicted using GalaxyTBM, and structure‐based template search was performed. If less than five oligomer templates were detected by the two template detection methods, the remaining homo‐oligomer models with the given oligomeric states were generated using an ab initio docking program GalaxyTongDock_C which predicts homo‐oligomer structures from the monomer structure using a grid‐based FFT docking method considering C n ‐symmetry. The models were further refined by loop/terminus modeling using GalaxyLoop and by overall relaxation using GalaxyRefineComplex .…”

“…The predicted subunit structures were docked to form complex structures by using the ab initio protein‐protein docking program GalaxyTongDock. GalaxyTongDock performs FFT‐based, low‐resolution protein‐protein docking with improved scoring function and selects docking poses after clustering . The GalaxyTongDock score is based on ZDOCK energy components, and the weight parameters were optimized by iterative docking and parameter search.…”

“…GalaxyTongDock performs FFT-based, low-resolution protein-protein docking with improved scoring function and selects docking poses after clustering. 17 The GalaxyTongDock score is based on ZDOCK energy components, 7,18,19 and the weight parameters were optimized by iterative docking and parameter search. Top 10 complex structures generated by GalaxyTongDock underwent optimization considering structure flexibility using GalaxyRefineComplex, 26 resulting in five final models.…”

“…We recently developed two server methods named GalaxyHomomer and GalaxyTongDock for protein oligomer structure prediction. GalaxyHomomer predicts homo‐oligomer structure via TBM and ab initio docking depending on the existence of proper oligomer templates.…”

“…Computational methods fill this gap by generating multimeric models for target proteins by template-based modeling (TBM), [4][5][6] ab initio docking, [7][8][9][10][11][12][13] or data-assisted complex modeling. [14][15][16] We recently developed two server methods named Gal-axyHomomer 5 and GalaxyTongDock 17 for protein oligomer structure prediction. GalaxyHomomer predicts homo-oligomer structure via TBM and ab initio docking depending on the existence of proper oligomer templates.…”