FireflyVina2LS

Marcus M. C. Ao & Shirley W. I. Siu

Computational Biology and Bioinformatics Lab (CBBio)
Department of Computer and Information Science (CIS)
University of Macau (UM)

http://cbbio.cis.umac.mo

RELEASE NOTES:

• FireflyVina2LS was developed based on the framework of PSOVina2LS.
  For more information about Vina, please visit http://vina.scripps.edu.

Instructions:

1. REQUIRED SOFTWARE

   For successful compilation, please install Boost (version 1.59.0)
   from http://www.boost.org. For preparing molecules for docking,
   please install AutoDockTools (ADT) from http://mgltools.scripps.edu.

2. INSTALLATION

   The installation basically follows the installation of AutoDock Vina.
   The steps are simple:

   a. unpack the files
   b. cd firevina2ls/build//release
   c. modify Makefile to suit your system setting
   d. type “make” to compile

   The binary firevina2ls 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.

3. RUNNING FireflyVina2LS

   You can run fireflyvina2ls as the way you run vina but additional four
   parameters (optional) are used to specify how the firefly algorithm performs
   searching:

   % /fireflyvina2ls

   Firefly parameters (optional):

   --num_fireflies arg (=16)     Number of fireflies
   --beta arg (=1)               Attractiveness
   --gamma arg (=1)              Absorption coefficient 
   --alpha arg (=0.9)           Randomization parameter 

   2LS parameters (optional):

   --Cr arg(=15)                 Roughing condition
   --R arg(=0.1)                 Roughing factor

   For example, docking Kifunensine in the Mannosidase enzyme (PDBID 1ps3 from
   the PDBbind v2012 dataset) using FireflyVina2LS with default firefly parameters in a
   8-core computer and return the lowest energy prediction:

   % /prepare_ligand4.py -l 1ps3_ligand.mol2 \
   -o 1ps3_ligand.pdbqt -A ‘hydrogens’ -U ‘nphs_lps_waters’

   % /prepare_receptor4.py -r 1ps3_protein.pdb \
   -o 1ps3_protein.pdbqt -A ‘hydrogens’ -U ‘nphs_lps_waters’

   % /fireflyvina2ls \
   —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

   If you have more CPUs, you can increase the number of fireflies,
   e.g. with availability of 16 CPU, try these options:

   —cpu 16 —num_fireflies 16

4. DEVELOP FireflyVina2LS

   If you are interested in the source code of FireflyVina2LS for any academic
   purposes, please note that the following files were newly developed
   in our work or modified based on FireflyVina:

   src/lib/quasi_newton.cpp

   src/lib/firefly_mutate.cpp

5. CITATION

   Please cite our paper if you have used FireflyVina2LS.
   M. C. Ao and S. W. I. Siu, “Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-Ligand Docking Program”,
   12th International Conference on Bioinformatics and Biomedical Technology (ICBBT2020).

6. CONTACT US

   Developer: Marcus M. C. Ao mingchi_@hotmail.com
   Project P.I.: Shirley W. I. Siu shirleysiu@umac.mo

   Computational Biology and Bioinformatics Lab, University of Macau
   http://cbbio.cis.umac.mo
   http://www.cis.umac.mo/~shirleysiu