Method for GalaxyRefine2

GalaxyRefine2 performs iterative optimization with various geometric operators to improve accuracy of the initial model. Compared to the previous method, GalaxyRefine, which relaxes an initial structure using MD and side chain perturbation, this method utilizes global operators (e.g. anisotropic normal mode perturbation and secondary structure perturbation) and local operators (e.g. loop modeling and hybridization), as well as local error estimation and homolog structure information, so that the accuracy of the structure could improve. Please note that slightly different results can be obtained in different runs because of the stochastic nature of the conformational search and optimization algorithm.

Inputs for GalaxyRefine2

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.
Currently, any monomer structure with sequence length upto 300 is allowed as an input.
Submitted protein structures should have no missing residues.

Refinement Options

This option controls the width of conformational search.
  • Default: Lorentzian function is used for weaker restraint. Conformational search is conducted more aggressively.
  • Conservative: Harmonic function is used for stronger restraint. Structures distant from the initial model are penalized.

Outputs for GalaxyRefine2

Predicted Structures

The 10 best models are shown. (Gray - Initial structure; Rainbow - Refined structure) You can also download the pdb files.

Structure Information

The models are listed in the order of GALAXY energy. Other model accuracy prediction scores such as QMEAN, ModFOLD, or ProQ3 may be consulted as supplementary scores.

Supplementary Information

Response time

Response time depends on the number of residues. Currently, time limit for each job is set to 10 hours. In most cases, the prediction is finished in 6-10 hours with 24 processors of Intel Xeon E5-2650 (2.20 GHz).

References for GalaxyRefine2
  • G. R. Lee, J. Won, L. Heo, and C. Seok*, GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure, Nuclear Acids Research, 47 (W1), W451-W455 (2019). [LINK]
  • G. R. Lee, L. Heo, and C. Seok*, Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment, Proteins: Structure, Function, and Bioinformatics, 86 (S1), 168-176 (2018). [PUBMED]