Small Molecule Docking

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ICM-Docking provides a unique set of tools for the modeling of protein/ligand interactions. Performs fast and accurate docking of fully continuously flexible small molecule ligands to a protein represented by grid interaction potentials. Allows users to dock the ligand to the explicit full-atom representation of the receptor with arbitrarily selected subset of flexible side-chains. Performs docking by the ICM stochastic global optimization procedure which combines pseudo-Brownian positional and torsional steps with fast local gradient minimization. Uses continuously differentiable grid potentials to ensure rapid convergence of local minimizations. Contains a sophisticated algorithm for tracking the simulation trajectory to avoid trapping in sub-optimal conformations and allows efficient search of the conformational space. Provides tools for automatic conversion of 2D chemical structures to 3D, sophisticated atom type assignment, charge assignment and recognition of rotatable bonds. Allows parts of the ligand to be automatically constrained to a pre-defined position during docking. Generates multiple conformations of the free or docked ligand. Special Monte-Carlo steps allow sampling of stereo isomers for racemic compounds. Analyzes protein surface for potential binding pockets and displays the interaction properties on the 'skin' representation of the surface. Uses graphical user interface for easy set up of the simulations. Provides maximum flexibility to user by allowing the docking scripts, which are written in intuitive ICM molecular modeling scripting language, to be modified to best meet specific project requirements. Performs protein-protein docking with fast global rigid-body search with grid potentials. Refines best docked configurations with flexible side chains to allow for the induced fit. Return to Main ICM-Pro Page

Key Small Molecule Docking Features

Interactive and Batch Docking

Dock chemicals in a loaded chemical spreadsheed automatically converted to 3D.

Dock a loaded ligand in 3D.

Dock directly from Mol or SDF file.

Dock up to 100 compounds at a time. If you need to dock more use ICM-VLS.

Change length of docking simulation (thoroughness)

Store alternative conformations.

Post-Docking

Multiple solutions ranked by energy.

Interactively browse docking hits.

Display ligand binding pocket whilst browsing.

Display dynamic hydrogen bonds whilst browsing.

Browse binding poses ranked by energy store in a stack.

Template Docking

Dock a ligand directly to a template small molecule in the binding site.

Template match method options: substructure, atom name, fuzzy or Atomic Property Field.

Dock to Electron Density

Methods for incorporating Induced Fit

Refine the ligand binding pocket with the bound ligand.

Multiple receptor docking (4D docking). Dock to many receptor conformation at one time to represent flexibility in the ligand binding site.

Docking Preferences

Sample racemic centers.

Sample double bond cis trans.

Relax covalent geometry.

Flexible ring sampling.

Keep carboxyls neutral.

Charge group options: none, NH2, NH2NH, NH@ NH NT, imidazole or auto.

A variey of binding site display options.

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