an ultra-high-performance protein-protein docking for heterogeneous supercomputers

Introduction

MEGADOCK 4.0 is a structural bioinformatics software for FFT-grid-based protein-protein docking that takes advantage of the massively parallel CUDA architechture of NVIDIA GPUs and multiple computation nodes.
MEGADOCK has been introduced to NVIDIA Corporation in the GPU-accelerated application catalog. (here)

Download

version 4.1.1: megadock-4.1.1.tgz (Apr 17, 2019 changed the sorting algorithm of docking scores)
GitHub repository is available from here.
(old versions of MEGADOCK were integrated into the current version.)

Requirements

• FFTW3 - http://www.fftw.org
  --enable-float flag must be specified when you compile FFTW3 (see also FAQ).
• OpenMPI - http://www.open-mpi.org (if you use MPI)
  
• CUDA Toolkit ver >= 5.0 - https://developer.nvidia.com/cuda-zone (if you use GPU)
  
• GPU Computing SDK code samples (CUDA SDK, same version as CUDA Toolkit) - https://developer.nvidia.com/cuda-zone (if you use GPU)

License

MEGADOCK is open source licensed under the GNU General Public License, version 3 or later.

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.

Developers

• Dr. Masahito Ohue (Tokyo Institute of Technology, Japan)
• Mr. Takanori Hayashi (Tokyo Institute of Technology, Japan)
• Mr. Hiroki Watanabe (Tokyo Institute of Technology, Japan)
• Prof. Yutaka Akiyama (Tokyo Institute of Technology, Japan)

Fundings

This work is partially supported by JSPS Grant-in-Aid for Scientific Research (KAKENHI) (24240044, 15K16081, 17H01814, 18K18149).

Contact

Please contact the below address in case you find a bug, need detailed information or others.
megadock @ bi.cs.[ti] (please replace [ti] with titech.ac.jp)