MEGADOCK - Akiyama Lab.

English/Japanese

A fft-based protein-protein docking system for all-to-all protein-protein interaction predictions.

MEGADOCK version 2.6 was integrated to current version (ver. 4.0).
http://www.bi.cs.titech.ac.jp/megadock/

Download

Ver. 2.6: megadock-2.6.tgz
(older version: here )

Requirements

MEGADOCK requires FFTW3 library. FFTW3 can be downloaded from http://www.fftw.org.
--enable-float flag must be specified when you compile FFTW3.

Installation

Extract tarball contents

    $ tar xzvf megadock-2.6.tgz
    $ cd megadock-2.6

Edit Makefile

Add your C++ compiler to the CC line
(ex. CC = g++ -fopenmp)
Add the path to your FFTW header files to the CFLAGS line
(ex. CFLAGS = -c -I/usr/local/include)
Add the path to your installation of FFTW library to the LDFLAGS line
(ex. LDFLAGS = -lm -L/usr/local/lib -lfftw3f)

Usage

Example:

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

Attention:

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

Options:

    -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

You need to run ZRANK on your docking output. ZRANK is available at: http://zlab.bu.edu/zdock/
Reference: Pierce B and Weng Z., A combination of rescoring and refinement significantly improves protein docking performance., Proteins, 72(1):270-279, 2008. [Paper]
Details on clustering and interaction prediction method, see:
Matsuzaki Y, Matsuzaki Y, Sato T, Akiyama Y., In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis., J Bioinform Comput Biol, 7(6):991-1012, 2009. [Paper]

Release notes

v2.6 : Added hydrophobic interaction score (based on [Ohue 2012]) (this version)
v2.3 : Corresponding to RNA/DNA molecules (based on [Ohue 2011])
v2.1 : rPSC+Elec score (link)
v2.0 : rPSC score
v1.0 : Katchalski-Katzir score

References

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), 776-778, 2014.
Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis. Lecture Note in Bioinformatics 7632 (In Proc. of PRIB 2012), 178-187, Springer Heidelberg, 2012.
SpringerLink
Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama. Docking-calculation-based Method for Predicting Protein-RNA Interactions. Genome Informatics, 25(1), 25-39, 2011.