GalaxyRefineComplex
Refinement of protein-protein complex model structures driven by interface repacking
0. Remark
The GalaxyRefineComplex distribution version supports only Linux 64-bit OS and binary files compiled with serial/parallel option.
1. Installation
- Download the GalaxyRefineComplex program
- Download a copy of GalaxyRefineComplex
- https://github.com/seoklab/GalaxyRefineComplex
- https://github.com/seoklab/GalaxyRefineComplex/archive/master.zip * Or, clone the GalaxyRefineComplex git repository
- git clone https://github.com/seoklab/GalaxyRefineComplex.git
- Unzip and place the downloaded files
- unzip GalaxyRefineComplex.zip
- mv GalaxyRefineComplex $GALAXY_HOME
(example: GALAXY_HOME=/applic/GalaxyRefineComplex)
- Execute install.sh
- $GALAXY_HOME/install.sh
- Check the downloaded files
- There should exist:
- bin: directory for executables
There should be build_initial_model, local_optimize, generate_model, and GalaxyRefineComplex - data: directory for data files
- examples: directory for example files
- Set environment variable
- export GALAXY_HOME=$GALAXY_HOME
(example: export GALAXY_HOME=/applic/GalaxyRefineComplex)
- export GALAXY_HOME=$GALAXY_HOME
- Find a proper GalaxyRefineComplex executable
- We supply two different GalaxyRefineComplex executables having compiled on different environments
- CentOS 6.6: bin/GalaxyRefineComplex.centos66
- Ubuntu 16.04 LTS: bin/GalaxyRefineComplex.ubuntu1604 * We have compiled Python scripts using PyInstaller, and it uses built-in Linux C libraries. Since, each computing environments may have different C libraries, so you need to find a working version with your environment. If both of them are not working, then please ask us with your computing environment.
- Set MPI environment (optional)
- GalaxyRefineComplex supports MPICH, so if you have installed MPICH, you can run it in parallel.
- GalaxyRefineComplex has been tested with MPICH hydra (http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz).
- You can use parallel version of GalaxyRefineComplex by setting EXEC_MPI environment
- (in BASH) export EXEC_MPI=$PATH_TO_THE_MPIEXEC (example: export GALAXY_HOME=/opt/mpi/mpich/bin/mpiexec) * You can set the number of CPU to use by setting NSLOTS environment
- (in BASH) export NSLOTS=8
- Since it will use CPUs up to the number of simulation trajectories (default=16 for each protocol), so we recommend you to set it one of the divisor (i.e., 4, 8, 16) to make it efficient.
2. How to use GalaxyRefineComplex
- Prepare the input protein structure in PDB format
- You have to provide a protein complex model in the PDB file format for complex refinement.
- Protein chains must have different chain IDs and be separated by “TER” line.
- Run GalaxyRefineComplex
- Usage: $GALAXY_HOME/bin/GalaxyRefineComplex [-h] [-p INPUT PDB File] [-t TITLE] [-f Sequence] [-s Number of samplings] [-o Number of outputs] [–sym] [–protocol1] [–protocol2]
- Input arguments and options:
- -p/–pdb: The input PDB file (mendatory)
- -t/–title: The title for a GalaxyRefineComplex job
- -f/–seq: The sequence for the PDB file in FASTA format
- -s/–n_sample: The number of sampling trajectories (default: 32=16x2)
- -o/–n_output: The number of refined outputs (default: 10=5x2)
- –sym: use symmetric refinement (default: False)
- –protocol1: use the protocol1 only (default: False)
- –protocol2: use the protocol2 only (default: False)
- Output of GalaxyRefineComplex
- The GalaxyRefineComplex generates a working directory, which is named by the job title (default: GalaxyRefineComplex)
- 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 GalaxyRefineComplex, refined protein model structures in PDB format will be placed.
* The final refined model will be ${JOB Title}/model/model_[1-10].pdb
3. Release log
- Jul, 2017: The first release of GalaxyRefineComplex
4. References
- L. Heo, H. Lee, and C. Seok, GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking, Sci. Rep. 6, 32153 (2016). [PUBMED]
5. Contact
- chaok@snu.ac.kr
- compbio.galaxy@gmail.com