GalaxyRefineComplex

Method for GalaxyRefineComplex

GalaxyRefineComplex is an extension of GalaxyRefine to protein-protein complexes by allowing flexibility at protein interfaces to capture conformational changes upon binding. You can download a standalone version at here.




Inputs for GalaxyRefineComplex

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.

Input Structure


You have to provide a protein structure in the PDB File Format for structure refinement.
Protein chains must have different chain IDs and be separated by "TER" line.
No gaps are allowed in the middle of input protein chains.


Refinement Option


  • Symmetric refinement for homo-oligomer (Default: No)
    • Yes: The input structure is refined keeping the initial symmetry of chains.
      To use this option, chains in the input MUST have identical sequences and nearly the same structures (TM-score > 0.9).
    • No : The input structure is refined with no consideration of symmetry.



Outputs for GalaxyRefineComplex

Predicted Structures


The 10 best models are shown. The initial complex structure is in grey, and refined models are in red to blue color. You can also download the pdb files.

Structure Information


Information on the global protein complex structure is provided in terms of interface area and the MolProbity score. The interface area is calculated by using the Naccess program. The MolProbity score reflects physical reality in terms of steric clashes, rotamer outliers, and phi/psi angles in Ramachandran favored region.


Structure change of each protein chain by refinement is reported in terms of backbone RMSD.


Ligand RMSD and interface area are reported. If there are more than 2 protein chains, information on all possible protein chain pairs are reported.

Download


Users can download 10 structures refined by GALAXY.




Supplementary Information

Response time


Response time linearly depends on the number of protein residues. In most cases, the refinement process is finished in 2 hours with 16 cores of Intel Xeon E5410 (2.33 GHz).




References for GalaxyRefineComplex
  • L. Heo, H. Lee, and C. Seok, GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking, Sci. Rep. 6, 32153 (2016). [PUBMED]
  • L. Heo, H. Park, and C. Seok, GalaxyRefine: Protein structure refinement driven by side-chain repacking, Nucleic Acids Res. 41 (W1), W384-W388 (2013). [PUBMED]