##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:
   • http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz
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

   • Download a copy of GalaxyPPDock
     • https://github.com/seoklab/GalaxyPPDock/archive/master.zip

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

• [email protected]
• [email protected]