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PSOVina2LS - A new approach enhances the time efficiency of a docking program by introducing a two-stage local search method 


Given a candidate solution, a rough local search is performed in the first stage to determine the potentiality of the solution. Only if the solution is promising, the second stage with a full local search will be performed. Our method has been realized in the PSOVina docking program and tested on two data sets. The experimental results show that two-stage local search achieves almost 2x speedup to conventional one-stage method, it also enhances the prediction performance of the docking method in terms of increased success rate and RMSD.


Version 1.0 (15 Jan 2017)

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

Required Software

For successful compilation, please install Boost (version 1.59.0). 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 psovina2ls_1.0/build/<your-platform>/release
c. modify Makefile to suit your system setting
d. type "make" to compile

The binary psovina2ls 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 PSOVina2LS

For example, docking Kifunensine in the Mannosidase enzyme (PDBID 1ps3 from the PDBbind v2012 dataset) using PSOVina2LS with default PSO parameters in a 8-core computer and obtain the lowest energy prediction:

% <path-to-AutoDockTools>/prepare_ligand4.py -l 1ps3_ligand.mol2 -o 1ps3_ligand.pdbqt -A 'hydrogens' -U 'nphs_lps_waters'

% <path-to-AutoDockTools>/prepare_receptor4.py -r 1ps3_protein.pdb -o 1ps3_protein.pdbqt -A 'hydrogens' -U 'nphs_lps_waters'

% <path-to-psovina2ls>/psovina2ls --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  --num_modes 1 --cpu 8

   More test cases can be available soon.

Develop PSOVina2LS

If you are interested in the source code of PSOVina2LS for any academic purposes, please note that the following files were newly developedin our work or modified based on Vina:
        psovina2ls_1.0/src/lib/quasi_newton.cpp
        psovina2ls_1.0/src/lib/pso_mutate.cpp


Citation

Please cite our paper if you have used PSOVina2LS. It would also be nice to let us know that you found PSOVina useful by sending us an email:
Allan H. Lin, Giotto H. K. Tai, and Shirley W. I. Siu*
Improving The Efficiency of PSOVina for Protein-Ligand Docking By Two-Stage Local Search
(Submitted)


Contact Us

Developer: Allan H. Lin   lhang33_[at]_126_[dot]_com

Giotto H. K. Tai
giottotai_[at]_yahoo_[dot]_com_[dot]_hk
Project P.I.: Shirley W. I. Siu shirley_siu_[at]_umac_[dot]_mo
(please remove all underscores)