GalaxyRefine: A program for protein structure model refinement
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README.md

README.md

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