PSOVina 1.0 – Fast Protein-ligand Docking tool based on PSO and AutoDock Vina

PSOVina 1.0

:: DESCRIPTION

PSOVina combines the particle swarm optimization (PSO) algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking.

::DEVELOPER

Computational Biology and Bioinformatics Lab (CBBio)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PSOVina

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2015 Jun;13(3):1541007. doi: 10.1142/S0219720015410073. Epub 2015 Feb 10.
PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.
Ng MC, Fong S, Siu SW.

SODOCK – Swarm Optimization for Flexible Protein-Ligand Docking

SODOCK

:: DESCRIPTION

SODOCK is an optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO is a population-based search algorithm.

::DEVELOPER

Intelligent Computing Lab. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SODOCK

:: MORE INFORMATION

Citation

J Comput Chem. 2007 Jan 30;28(2):612-23.
SODOCK: swarm optimization for highly flexible protein-ligand docking.
Chen HM1, Liu BF, Huang HL, Hwang SF, Ho SY.

GRAMM 1.03 / GRAMM-X – Protein-Protein Docking and Protein-Ligand Docking

GRAMM 1.03 / GRAMM-X

:: DESCRIPTION

GRAMM (Global Range Molecular Matching) is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc.

::DEVELOPER

Vakser Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 GRAMM

:: MORE INFORMATION

Citation:

GRAMM-X public web server for protein-protein docking.
Tovchigrechko A, Vakser IA.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W310-4.