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GWOVina - Fast Protein-Ligand Docking Tool based on GWO and AutoDock Vina 


Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. Based on the implementation of AutoDock Vina, GWOVina employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses. Our rigid docking experiments show that GWOVina has enhanced exploration capability leading to significant speedup in the search while maintaining comparable binding pose prediction accuracy to AutoDock Vina. For flexible receptor docking, GWOVina is also competitive in pose ranking. Its success rate is higher than AutoDock Vina, but similar to AutoDockFR.

Releases

Download

(Freely available for research only, please read our Open Source License)

Required Software

For successful compilation, please install Boost (version 1.59 or above). For preparing molecules for docking,  please install AutoDockTools (ADT).

Installation

The installation basically follows the installation of AutoDock Vina:
a. unpack the files
b. cd gwovina-x.x/build/<your-platform>/release
c. modify Makefile to suit your system setting
d. type "make" to compile

The binary gwovina will be generated at the current directory. You can copy this binary to a directory in your PATH e.g. /usr/local/bin, or add the path of the current directory to your PATH.

Running GWOVina

You can run gwovina as the way you run vina but an additional parameter to specify the population size can be given:
--num_wolves arg (=12) Number of wolves

For example, docking Kifunensine in the Mannosidase enzyme (PDBID 1ps3 from the PDBbind v2012 dataset) using GWOVina:

% <path-to-AutoDockTools>/prepare_ligand4.py -l 1ps3_ligand.mol2 -o 1ps3_ligand.pdbqt

% <path-to-AutoDockTools>/prepare_receptor4.py -r 1ps3_protein.pdb -o 1ps3_protein.pdbqt

% <path-to-gwovina>/gwovina --receptor 1ps3_protein.pdbqt --ligand 1ps3_ligand.pdbqt  --center_x  31.951 --center_y 65.5053 --center_z 7.63888 --size_x  33.452 --size_y 27.612  --size_z  35.136  

Develop GWOVina

If you are interested in the source code of GWOVina for any research purposes, please note that the following files were newly developed in our work or modified based on Vina:
        gwovina-x.x/src/main/main.cpp
        gwovina-x.x/src/lib/gwo.h
        gwovina-x.x/src/lib/gwo.cpp
        gwovina-x.x/src/lib/parallel_gwo.h
        gwovina-x.x/src/lib/parallel_gwo.cpp
        gwovina-x.x/src/lib/gwo_mutate.h
        gwovina-x.x/src/lib/gwo_mutate.cpp


Citations

Please cite our paper if you have used GWOVina or its variants. It would also be nice to let us know that you found GWOVina useful by sending us an email:

For GWOVina 1.0:
Kin Meng Wong, Hio Kuan Tai, and Shirley W. I. Siu*. Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking. (Submitted)


Contact Us

Developer: Michael Wong emailtoming15_[at]_hotmail_[dot]_com
Project P.I.: Shirley W. I. Siu shirley_siu_[at]_umac_[dot]_mo
(please remove all underscores)