A fast protein-protein docking software on GPUs.
MEGADOCK-GPU version 1.0 was integrated to current version (ver. 4.0).


Ver. 1.0: megadock-gpu-1.0.tgz


MEGADOCK-GPU requires nVIDIA's GPUs which are capable for CUDA and the following libraries.


Extract tarball contents

    $ tar xzf megadock-gpu-1.0.tgz
    $ cd megadock-gpu-1.0

Edit Makefile



    $ ./megadock-gpu -R receptor.pdb -L ligand.pdb -o dock
    $ perl create.pl dock.out


receptor.pdb, ligand.pdb and create_lig must be in your current directory when you try to create all predicted structures using create.pl.


    -R filename    : receptor pdb file
    -L filename    : ligand pdb file

    -o filename    : set the output filename (default to "$R-$L.out")
    -O             : output the detail file named "[filename].detail" (default to none)
    -N integer     : set the number of output predictions (default to 2000)
    -t integer     : set the number of predictions per each rotation (default to 1)
    -F integer     : set the number of FFT point (default to none)
    -v float       : set the voxel size (default to 1.2)
    -D             : use 6 degree rotation (54000 rotations) instead of 15 degree (3600 rotations)
    -e float       : set the electrostatics term ratio (default to 1.0)
    -d float       : set the hydrophobic term ratio (default to 1.0)
    -a float       : set the rPSC receptor core penalty (default to -45.0)
    -b float       : set the rPSC ligand core penalty (default to 1.0)
    -f 1/2/3       : set function
                     (1: rPSC, 2: rPSC+Elec, 3: rPSC+Elec+Hydrophobic, default to 3)
    -h             : show the help messeage

Thread parallelization:

MEGADOCK can parallelize rotation calculations by using OpenMP. You can tell MEGADOCK the number of OpenMP threads you want to use by environmental variable such as $OMP_NUM_THREADS.

About post process and interaction prediction


Copyright © 2013 Akiyama Laboratory, Tokyo Institute of Technology, All Rights Reserved.
Last update : 2013/6/3