MEGADOCK 4.0 is a structural bioinformatics software for FFT-grid-based protein-protein using MPI/OpenMP/GPU parallelization.
| Type | Environment | Parallelization |
|---|---|---|
| (a) | GPU cluster | GPU, MPI + OpenMP |
| (b) | CPU cluster | MPI + OpenMP |
| (c) | GPU single node | GPU |
| (d) | CPU single node | OpenMP |
| Libraries | GPU cluster | CPU cluster | GPU | CPU | Notes |
|---|---|---|---|---|---|
| FFTW3 | x | x | x | x | --enable-float flag required (see FAQ) |
| OpenMPI | x | x | |||
| CUDA Toolkit | x | x | ver >= 5.0 required |
||
| CUDA SDK code samples | x | x | same version as CUDA Toolkit |
Please read appropriate documents for your environment.
- Prebuild image : akiyamalab/megadock (Docker Hub)
- Build from Dockerfile : Dockerfiles/README.md
Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, Bioinformatics, 30(22): 3281-3283, 2014. http://dx.doi.org/10.1093/bioinformatics/btu532
Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data, Protein and Peptide Letters, 21(8): 766-778, 2014. http://eurekaselect.com/112757
For older versions are available here.
http://www.bi.cs.titech.ac.jp/megadock/archives/
MEGADOCK is open source licensed under the GNU General Public License, version 3 or later.
This work is partially supported by JSPS Grant-in-Aid for Scientific Research (KAKENHI) (A) Grant Number 24240044.
Copyright © 2014-2018 Akiyama Laboratory, Tokyo Institute of Technology, All Rights Reserved.