ICM-Docking

ICM-Docking and chemistry module provides access to the chemical information and provides a unique set of tools for accurate individual ligand-protein docking, peptide-protein docking, and protein-protein docking, including interactive graphics tools. With the ICM-Dock module, you can do rapid and accurate docking simulations. The ICM-Pro GUI interface offers a step-by-step docking menu that makes docking easier than ever. To achieve your docking goals, ICM-Dock does the following:

Automatic preparation of a molecule for a flexible docking
Assignment of the MMFF atom types based on local connectivity
Addition of hydrogens
Assignment of partial charges
Automatic identification of rotatable bonds
Fast grid potentials
Scripting for small scale flexible ligand docking
Procedures for protein-protein docking
Procedures for flexible peptide-receptor docking
2D representations (SMILES): export and import,
Automatic 2D to 3D conversion
Refinement of docking solutions in full atom representation
Graphics Support for Virtual Ligand Screening Module (module requires special VLS license)

The ICM docking module also allows for the browsing of docking solutions, binding site analysis, visualization of grid potentials, adjustment of grid potential areas, and configurable preferences for ligand size and score threshholds.

Protein-Protein Docking:

In the case of docking two proteins, ICM was used to dock ab initio a full-atom model of lysozyme to an antibody with 1.6A accuracy (Nature Struc.Biol., 1994, 1,259). Later, Maxim Totrov and Ruben Abagyan correctly predicted the association of beta-lactamase and its protein inhibitor in the Docking Challenge (Nature Struc.Biol., 1996,3,290) using the ICM pseudo-Brownian docking with subsequent ICM side-chain refinement.

Docking a flexible ligand to a receptor:

A short flexible peptide can be docked with ICM to the surface of the protein with no restraints as was demonstrated for the SH2 and PTB domain ligands (Folding & Design, 1998, 3, 513) and cholera-toxin-derived peptide and an antibody (Structure, 1999, 7, 663). The ICM OBMCM global optimization method is used in combination with the grid description of the receptor potential.

Platforms Available : Windows 7/Vista/XP/NT/2000, Linux/i386/AMD64, SGI IRIX, Mac OS X