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GalaxyRefine

GalaxyRefine: A program for protein structure model refinement

#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

##4. References

##5. Contact