LZerD / Multi-LZerD / PI-LZerD – (Multiple) Protein-Protein Docking Algorithm

LZerD / Multi-LZerD / PI-LZerD

:: DESCRIPTION

LZerD: Protein-Protein Docking Algorithm

Multi-LZerD: protein docking for asymmetric complexes

PI-LZerD: Protein Docking Prediction Using Predicted Protein-Protein Interfaces

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

  LZerD / Multi-LZerD / PI-LZerD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Jan 10;13:7. doi: 10.1186/1471-2105-13-7.
Protein docking prediction using predicted protein-protein interface.
Li B1, Kihara D.

Proteins. 2012 Jul;80(7):1818-33. doi: 10.1002/prot.24079. Epub 2012 May 8.
Multi-LZerD: multiple protein docking for asymmetric complexes.
Esquivel-Rodríguez J1, Yang YD, Kihara D.

BMC Proc. 2012 Nov 13;6 Suppl 7:S4. doi: 10.1186/1753-6561-6-S7-S4. Epub 2012 Nov 13.
Effect of conformation sampling strategies in genetic algorithm for multiple protein docking.
Esquivel-Rodríguez J1, Kihara D.

Methods Mol Biol. 2014;1137:209-34. doi: 10.1007/978-1-4939-0366-5_15.
Pairwise and multimeric protein-protein docking using the LZerD program suite.
Esquivel-Rodriguez J1, Filos-Gonzalez V, Li B, Kihara D.

BDOCK – Grid-based Protein-protein Docking software

BDOCK

:: DESCRIPTION

BDOCK is a novel enzyme-inhibitor docking algorithm based on the degree of burial and conservation of surface residues

::DEVELOPER

Dr. rer. nat. Bingding Huang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • The FFTW library
  • The BALL library

:: DOWNLOAD

  BDOCK

:: MORE INFORMATION

Citation

Gene. 2008 Oct 1;422(1-2):14-21. doi: 10.1016/j.gene.2008.06.014. Epub 2008 Jun 14.
Using protein binding site prediction to improve protein docking.
Huang B, Schroeder M.

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.