No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
bin
data
examples
lib
templates
LICENSE
README
README.md
run.py

README.md

GalaxyPPDock: A program for protein-protein docking based on cluster-guieded conformational space annealing.

##0.Remark The GalaxyPPDock distribution version supports only Linux 64-bit OS and binary files compiled with MPI option. Linux 32-bit OS or binary files compiled with serial option are not supported. GalaxyPPDock takes receptor pdb file, ligand pdb file, and ZDOCK output file. Optionally, you can use PSSM(Position-Specific Scoring Matrix) for more accurate protein-protein docking.

##1. Installation GalaxyPPDock is only working Linux 64-bit system and binary files compiled with MPI option. Please install mpich2 first before running GalaxyPPDock.

##################################################################################### 1-1. Install mpich2 ####################

  1. Download mpich from:
  2. Unzip and place the download files
    • tar -xvzf hydra-3.2.tar.gz
  3. Move hydra MPI directory
    • cd hydra-3.2
  4. Add environment variables in $HOME/.bashrc
    • export LD=ld
  5. Configure mpich
    • ./configure
  6. Install mpich
    • make

You can find mpiexec.hydra file in the current directory.

##################################################################################### 2-1. Running GalaxyPPDock ####################

  1. Download the GalaxyPPDock program

  2. Unzip and place the downloaded files

    • unzip master.zip
  3. Check the downloaded files

    • There should exist:
      • bin: directory for executables
        There should be add_miss, energy_ligprotein, ppdock_opt.mpi, and ppdock_csa.mpi
      • data: directory for data files
      • examples: directory for example files
  4. Add environment variables in $HOME/.bashrc

    • export GALAXYPPDOCK_HOME=$HOME/GalaxyPPDock-master
    • export EXEC_MPI=$HOME/hydra-3.2/mpiexec.hydra
    • (example: export GALAXYPPDOCK_HOME=/applic/GalaxyPPDock-master)
    • (example: export EXEC_MPI=/applic/hydra-3.2/mpiexec.hydra)
  5. Move GalaxyPPDock example directory

    • cd $GALAXYPPDOCK_HOME/examples/1cgi (or 1eaw, TA12)
  6. Running GalaxyPPDock

    • ../../run.py receptor.pdb ligand.pdb zdock.out (default option)

    (other options)

    • ../../run.py receptor.pdb ligand.pdb zdock.out -pssm receptor.pssm ligand.pssm (using PSSM file)
    • ../../run.py receptor.pdb ligand.pdb zdock.out -n 50 (using multiple core, default=2)
  7. Output files of GalaxyPPDock

    • model01.pdb ~ model10.pdb files are protein complex structure models generated by GalaxyPPDock.

##3. Release log

  • 06 Mar 2016: The first release of GalaxyPPDock

##4. References

  • H. Lee, H. Park, J. Ko, W.-H. Shin, and C. Seok, GalaxyPPDock: Protein-protein docking by cluster-guided conformational space annealing, in preparation.

##5. Contact