MEGADOCK

MEGADOCK is an ultra-high-performance protein-protein prediction software for heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU parallelization.

Target Environments

| Type | Target Env. | Approach | |:----:|-----------------|--------------------| | (a) | GPU cluster | GPU + OpenMP + MPI | | (b) | CPU cluster | OpenMP + MPI | | (c) | GPU node | GPU + OpenMP | | (d) | CPU node | OpenMP |

Installation and Command Details

For installation and command details, please read appropriate section on followings:

• Read command and script details
  • doc/README.md
• Build a binary from source code
  • doc/BUILD.md
• Build a docker container image
  • doc/README_for_docker.md
    • akiyamalab/megadock (Docker Hub)

Reference

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://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. https://doi.org/10.2174/09298665113209990050

Older Versions

http://www.bi.cs.titech.ac.jp/megadock/archives/

License

MEGADOCK is licensed by CC BY-NC 4.0. (See LICENSE) This software and derivatives are NOT allowed for any commercial use without formal prior authorization. If you are considering commercial use, please contact us as there are differently charged use options licensed by Ahead Biocomputing, Co. Ltd., a private company as a Tokyo Tech Venture.

Fundings

This work is partially supported by JSPS Grant-in-Aid for Scientific Research (KAKENHI) (A) Grant Number 24240044.

---

Copyright © 2014-2022 Akiyama Laboratory, Tokyo Institute of Technology, All Rights Reserved.