GalaxyTongDock_D

Method for GalaxyTongDock_D

GalaxyTongDock_D performs ab-initio D symmetric homo-oligomer structure prediction with given monomer structure and oligomeric state. Experimental and/or evolutionary information can be utilized using block and interface options.


Inputs for GalaxyTongDock_D

User Information

First, you have to enter the following information required for modeling.
  • Job name: Enter job name for your recognition.
  • E-mail address: GalaxyWEB server will send progress reports of your job.

GalaxyTongDock_D Input


You have to provide a protein structure in the PDB File Format in the ascending order of residue numbers.
Oligomeric state should also be assigned. For example, oligomeric state of D3 symmetric homo-oligomer is 6.

Options for assigning block residues


Block option can be used to specify residues that should not be at the interface. The specified residues are blocked from the interface by large penalty score during docking.

Residue numbers should be separated by commas. Hyphen (-) can be used when you want to designate long sequential residues. For example, 52-60 is equivalent to 52,53,54,55,56,57,58,59,60.

Options for assigning interface residues


You can assign interface residues. C-Interface are used during C-symmtric structure (half of D-symmetric structure) building, and D-Interfaces are used during D-symmetric sturcutre building (1-D docking between two C-symmtric structures). You can fill C(D)-Interface n(1~5) only or both of C(D)Interface n and Partner n in each of interface. When only C(D)Interface n blank is filled, the designated residues will be on the interface of output structures. When you fill both blanks, the residues in C(D)-Interface n and residues in Partner n will make contact (< 8A) in the output structures.

Residue numbers should be separated by commas. Hyphen (-) can be used when you want to designate long sequential residues. For example, 52-60 is equal to 52,53,54,55,56,57,58,59,60.

Example)
C-interface1  [12,15-18,21] ,   Partner1 []
-> Residue 12,15,16,17,18,21 will be on interface during C-symmetric structure building.

C-interface2  [112,116]    ,   Partner2 [31,32]
-> Residue 112,116 and Residue 31,32 will make contact during C-symmetric structure building.

D-interface1  [41]         ,   Partner1 [61]
-> Residue 41 and Residue 61 will make contact during D-symmetric structure building.

D-interface2  [233]        ,   Partner2 []
-> Residue 233 will be on interface in during D-symmetric structure building.


Outputs for GalaxyTongDock_D

Predicted Models


The 10 models are shown in PV. Each model is downloadable. Predicted oligomer structures are described with green and one subunit is highlighted with purple color.


When the block and interface options are used, block and interface residues are described with red and blue colors, respectively.

TongDock_D Scores


The higher is the better score.

Download


TongDock_D Models (up to 50 models) can be downloaded. There is TongDock_D score for each model in the PDB file.



References for GalaxyTongDock_D
  • Park T, Baek M, Lee H, Seok C. GalaxyTongDock: symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters. J Comput Chem. 2019;40:2413-2417.