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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

  1. Download the GalaxyRefine program

  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