MEGADOCK-K (MEGADOCK on K computer)

A fft-based protein-protein docking system for all-to-all protein-protein interaction predictions. This release assumes running MEGADOCK on K computer, RIKEN, Japan. You can compile and run the program on other cluster systems by modifying parameters in Makefile.

Email: megadock at bi.cs.titech.ac.jp

Download

megadock-k-3.0.tgz

Requirements

MEGADOCK requires FFTW3 library. FFTW3 can be downloaded from http://www.fftw.org. You can use pre-built package installed on K computer. See detail on the manual of K computer.

Build

Read environmental variables

$ source /work/system/Env_base

Extract tarball contents

$ tar xzf megadock-k-3.0.tgz
$ cd megadock-k-3.0

Compile

$ make

An executable file 'megadockdp' will be generated. When you don't need MPI functionality, edit Makefile and set USE_MPI variable undefined. In this case a binary file 'megadock' will be generated for the use on single node systems.

Usage

Example:

$ ./megadockdp -rt 0 -tb sample.list

Parameters:

* Required
-tb [docking job table] 

* Optional
-lg [log file name]
-rt [number of retries] Number of retry of a docking 
    job if fails (defalt: 10)

Docking job table

Parameters and docking target list should be written in a text file. A table file should have "TITLE" and "PARAM" lines followed by parameters listed by the same order as in the "PARAM" line. "sample.list" file in this package shows an example.

Docking parameters

You can specify docking parameters loaded by MEGADOCK by setting 'PARAM' in the table file. Lines follows the 'PARAM' lines specifies parameters for each docking job which will be distributed to available nodes by MPI.

* Required
-R [receptor pdb file]
-L [ligand pdb file]

* Optional
-o [output filename] (default: receptor-ligand.out)
-D Use 6 degree rotation (54000 rotations) of ligand proteins 
   instead of 15 degree (3600 rotations)
-N [number of decoys] (default: 2000)
-e [Ratio of electrostatistics score to rPSC score] 
   (default: 1.0, strong elec: 1.25)
-f [Score function] Currently 1 (rPSC+CHARMM) and 2 (rPSC)
   are available (default: 1)
-t [number of decoys sampled per rotation] (default: 1)
-v [voxel pitch size] (default: 1.2 angstrom)

Docking output

Each docking job generates docking output file in which rotation angles (x, y, z) of ligand from the initial structure, numbers of voxel translation (x, y, z) from receptor center coordinate and docking scores are listed.