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A program for filling up the missing part of protein structure
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example added optional arguments: -o and -t Apr 9, 2016
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README.md

README.md

#GalaxyFill: A program for filling up the missing part of protein structure

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

##2. How to use GalaxyFill

  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 GalaxyFill
  • Usage: $GALAXY_HOME/bin/GalaxyFill [-h] [-p INPUT PDB File] [-s INPUT FASTA File]
  • Input arguments and options:
    • -p or --pdb : Input protein structure file in PDB format (mendatory)
    • -s or --seq : Input protein sequence file in FASTA format (mendatory)
    • -o or --out : Output protein structure file name (optional, default=${Input PDB prefix}_fill.pdb)
    • -t or --title : Running title for GalaxyFill (optional, default=${Input PDB prefix})
  1. Output of GalaxyFill
  • The final refined model will be ${Input PDB prefix}_fill.pdb or designated by "-o/--out" option

##3. Release log

  • 10 Apr 2016: Local energy optimization on the filled residues
  • 09 Apr 2016: Added optional arguments: -o and -t
  • 01 Feb 2016: The first release of GalaxyFill

##4. References

  • E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A Kinematic View of Loop Closure, J. Comput. Chem. 25, 510-528 (2004).

##5. Contact

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