#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

1. 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
2. Unzip and place the downloaded files
   • unzip GalaxyRefine.zip
   • mv GalaxyRefine $GALAXY_HOME
     (example: GALAXY_HOME=/applic/GalaxyRefine)
3. Check the downloaded files
   • There should exist:
   • bin: directory for executables
     There should be build_initial_model, local_optimize, generate_model, and GalaxyRefine
   • data: directory for data files
   • examples: directory for example files
4. Set environment variable
   • export GALAXY_HOME=$GALAXY_HOME
     (example: export GALAXY_HOME=/applic/GalaxyRefine)

##2. How to use GalaxyRefine

1. 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.
2. 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)
3. 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]

##5. Contact

• chaok@snu.ac.kr
• compbio.galaxy@gmail.com