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MEGADOCK 2.1

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

Download

Ver. 2.1: megadock-2.1.tgz

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 xzf megadock-2.1.tgz
    $ cd megadock-2.1

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 megadock.out
    $ perl create.pl megadock.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 [receptor pdb file]
    -L [ligand pdb file]
    -o [output filename] (default: receptor-ligand.out)
    -D use 6 degree rotation (54000 rotations) instead of 15 degree (3600 rotations)
    -N [number of decoys] (default: 2000)
    -t [number of decoys sampled per rotation] (default: 1)

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]