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

By Taeyong Park, Minkyung Baek, Hasup Lee, Chaok Seok. 2019

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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.

Subfields: Computational Theory and Mathematics, Molecular Biology