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
- Or, clone the GalaxyRefine git repository
-
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)
- export GALAXY_HOME=$GALAXY_HOME
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)
- -p or --pdb : Input protein structure file to refine (mendatory)
-
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.
- init: A working directory for cleaning up the input PDB file after initial side-chain optimization is performed.
- 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]