GalaxyWEB

Homo-oligomer structure of a protein with D_n symmetry is predicted. Docking of a monomer (subunit 1) and a copy of monomer (subunit 2) is performed first, structures for half (C_n symmetry) of the full oligomer are constructed from that, and two half structures (half 1 and half 2) are docked to form D_n symmetry. Use GalaxyTongDock_C for C_n symmetry.

User Information
Job name
E-mail address (Optional)

Protein Information
Monomer structure (≤1000 AA)	Protein Structure File (allowed file extensions: pdb, txt)
Oligomeric state (≤12)	Number of monomers. For example, oligomeric state of D2 symmetry is 4.
Block (Optional)
Block residues
	Residue numbers or residue ranges (e.g. 52-60) should be separated by commas. (example: 18,52-60,78,111-131)
C-Interface (Optional)
C-Interface 1	subunit 1 , subunit 2
C-Interface 2	subunit 1 , subunit 2
C-Interface 3	subunit 1 , subunit 2
C-Interface 4	subunit 1 , subunit 2
C-Interface 5	subunit 1 , subunit 2
	The number of specified residues for each of subunit 1 and subunit 2 should be less than 200. Residue numbers or residue ranges (e.g. 52-60) should be separated by commas. (example: 18,52-60,78,111-131)
D-Interface (Optional)
D-Interface 1	half 1 , half 2
D-Interface 2	half 1 , half 2
D-Interface 3	half 1 , half 2
D-Interface 4	half 1 , half 2
D-Interface 5	half 1 , half 2
	The number of specified residues for each of half 1 and half 2 should be less than 200. Residue numbers or residue ranges (e.g. 52-60) should be separated by commas.

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Help

• Information
• PDB File: File Format
• E-mail: Average run time is 1h. If e-mail address is given, the server sends notifications automatically. If not, the user has to bookmark the report page address.
• Block: Specified residues are blocked from the interface.
• C-Interface: Specified residues in this option are used when structure with C_n symmetry is predicted. The residues are preferred to be at the interface. If interface residues are provided for both subunit 1 and subunit 2, docking poses with those residues in contact are preferred. If interface residues are provided for only one subunit, those residues are preferred to be at the interface.
• D-Interface: Specified resiudes in this option are used when structure with D_n symmetry is predicted. The residues are preferred to be at the interface. If interface residues are provided for both half 1 and half 2, docking poses with those residues in contact are preferred. If interface residues are provided for only one 'half', those residues are preferred to be at the interface. See help page for details.

Example

• Monomer structure: Monomer.pdb
• Oligomeric state: 6
• No residues are specified for Block or Interface.
• Report: [View]