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GalaxyRefine

GalaxyRefine: program for protein structure model refinement

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GalaxyRefine: A program for protein structure model refinement

0. Remark

The GalaxyRefine distribution version supports only Linux 64-bit OS and binary files compiled with serial option. Linux 32-bit OS or binary files compiled with MPI option are not supported.

1. Installation

Download the GalaxyRefine program
- Download a copy of GalaxyRefine
  - https://github.com/seoklab/GalaxyRefine
  - https://github.com/seoklab/GalaxyRefine/archive/master.zip
- Or, clone the GalaxyRefine git repository
  - git clone https://github.com/seoklab/GalaxyRefine.git
Unzip and place the downloaded files
- unzip GalaxyRefine.zip
- mv GalaxyRefine $GALAXY_HOME
  (example: GALAXY_HOME=/applic/GalaxyRefine)
Check the downloaded files
- There should exist:
- bin: directory for executables
  There should be build_initial_model, local_optimize, generate_model, and GalaxyRefine
- data: directory for data files
- examples: directory for example files
Set environment variable
- export GALAXY_HOME=$GALAXY_HOME
  (example: export GALAXY_HOME=/applic/GalaxyRefine)

2. How to use GalaxyRefine

Prepare the input protein structure in PDB format
- You have to provide a protein structure in the PDB file format for structure refinement. Gaps (or chain breaks) are highly prohibited in the middle of the initial protein structure.
Run GalaxyRefine
- Usage: $GALAXY_HOME/bin/GalaxyRefine [-h] [-p INPUT PDB File] [-t TITLE] [-s N_sample] [-o N_output]
- Input arguments and options:
  - -p or --pdb : Input protein structure file to refine (mendatory)
  - -t or --title : The refinement job title (default: GalaxyRefine)
  - -s or --n_sample : The number of simulation trajectories for sampling (default: 16)
  - -o or --n_output : The number of refined output models (default: 5)
Output of GalaxyRefine
- The GalaxyRefine generates a working directory, which is named by the job title (default: GalaxyRefine)
- In the working directory, the following three directories will be generated:
  - init: A working directory for cleaning up the input PDB file after initial side-chain optimization is performed.
  - refine: A working directory for refining protein structure model with SC perturbations and MD relaxations.
  - model: The output of GalaxyRefine, refined protein model structures in PDB format will be placed.
- The final refined model will be ${JOB Title}/model/model.pdb

3. Release log

01 Feb 2016: The first release of GalaxyRefine

4. References

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]
G. R. Lee, L. Heo, and C. Seok, Effective protein model structure refinement by loop modeling and overall relaxation, Proteins: Structure, Function, and Bioinformatics, in press (2015). [PUBMED]