ICM-Pro

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract ICM-Pro (Internal Coordinate Mechanics-Pro) is an easy-to-use and complete desktop-modeling environment for a biologist or a chemist interested in molecular structure and function. It empowers them with fast access and high quality interactive 3D views to the entire structural database.

In just a few seconds you can browse hundreds of structures of interest, load them, analyze and visualize sequences, structures, alignments, sites, study pockets and bound ligands and drugs, study surfaces, electrostatics, mutations, sequence conservations, perform docking of small molecules as well as protein-protein docking.

ICM-Pro supports multiple input formats. You can search the structural database by field, sequence pattern, and get an interactive table for instant viewing. It offers a rich graphical environment and advanced views for professional quality images and molecular animation videos.

Protein Structure Analysis -- ICM-Pro provides a direct link to the Protein Data Bank (PDB). Once you have downloaded a structure you can analyze the structure - flagging problem regions, superimpose multiple structures, analyze distances and angles, calculate contact and surface areas and electrostatic properties, etc.

Key Protein Structure Analysis Features include:

Dynamic link to the Protein Data Bank, PDB File Preparation, Protein Superposition, Calculate Contact Area, Calculate Surface Area, Measure and Display Distances and Angles;

Ramachandran Plots, Drug Binding Pocket and Cavity Identification, Protein-Protein Interaction Site Prediction, Protein Health, Predict Side Chain Flexibility, and Protein-Ligand Interactions.

Crystallographic Analysis Tools -- The key to understanding a protein structure is to fully evaluate the underlying crystallographic information contained within a PDB file.

For example, it is important to understand the full biological unit of a protein to identify if crystal-crystal contacts have influenced the structure or for example, contour the electron density to see how much of a ligand was seen by the crystallographer in the active site.

Key Crystallographic Analysis Features include:

Crystallographic Neighbor, Crystallographic Cell, Biomolecule Generator, and Electron Density Maps.

Small Molecule Docking -- ICM-Pro provides a unique set of tools for the modeling of protein/ligand interactions. It performs fast and accurate docking of fully, continuously flexible small molecule ligands to a protein represented by grid interaction potentials. There are also built-in procedures to account for induced fit which includes multiple receptor docking (4D docking) and explicit receptor docking.

ICM-Pro allows users to dock the ligand to the explicit full-atom representation of the receptor with an arbitrarily selected subset of flexible side-chains. It performs docking by the ICM stochastic global optimization procedure which combines pseudo-Brownian positional and torsional steps, with fast local gradient minimization. It uses continuous differential grid potentials to ensure rapid convergence of local minimizations.

ICM-Pro contains a sophisticated algorithm for tracking the simulation trajectory to avoid trapping in sub-optimal conformations and allows efficient search of the conformational space. It provides tools for the automatic conversion of 2D chemical structures to 3D, sophisticated atom type assignment, charge assignment and recognition of rotatable bonds.

ICM-Pro allows parts of the ligand to be automatically constrained to a pre-defined position during docking. It generates multiple conformations of the free or docked ligand.

Special Monte-Carlo steps allow sampling of stereo isomers for racemic compounds. It analyzes the protein surface for potential binding pockets and displays the interaction properties on the ‘skin’ representation of the surface.

It uses a graphical user interface (GUI) for easy set up of simulations. ICM-Pro provides maximum flexibility to the user by allowing the docking scripts, which are written in the ICM molecular modeling scripting language, to be modified to best meet specific project requirements.

ICM-Pro performs protein-protein docking with a fast global rigid-body search with grid potentials. It refines best docked configurations with flexible side chains to allow for the induced fit.

Key Small Molecule Docking Features include:

Interactive and Batch Docking, Post-Docking, Template Docking, Dock to Electron Density - Methods for incorporating Induced Fit, and Docking Preferences.

Protein-Protein Docking -- ICM-Pro contains a well validated and successful protein-protein docking algorithm. ICM-Pro has consistently performed very well at the worldwide CAPRI protein-protein docking competition. ICM-Pro also contains an algorithm to predict protein-protein docking interaction sites.

Key Protein-Protein Docking Features include:

Protein-Protein Interaction Site Prediction - Protein-protein interaction site prediction using the ICM Optimal Docking Area (ODA) method; Color the protein by protein-protein interaction hotspots; and tabulate the ODA prediction for each residue in a fully-interactive table.

Protein-Protein Docking - Dock to specific epitopes on the surface of the receptor; Sample only specific epitope sites on the ligand; Dock to the whole receptor (if No binding site is predicted); Flexible ligand and receptor represented by maps; Flexible ligand-receptor refinement; Run multiple jobs on different machines in a cluster;

Ranked results table with energy values displayed including - van der Waals grid potential, hydrogen bonding grid potential, electrostatics grid potential, hydrophobic potential, polar terms of the solvation energy, aliphatic terms of the solvation energy, aromatic terms of the solvation energy and a weighted total of the solvation energy terms.

Bioinformatics Tools -- ICM-Bioinformatics is included in the ICM-Pro package and it allows users to search a sequence database with high-quality global pairwise and multiple alignment algorithms.

It also allows pattern searches, PROSITE - (PROSITE is a protein database) and profile searches. Its multiple sequence alignments are fast, the algorithm produces evolutionary trees, principal component view, annotation transfer from sequence to structures, threading and includes alignment visualization tools.

Sequence Analysis - Find alternative alignments and repeats using filtered and probability based dot-plot. Make accurate pairwise sequence alignment with a double affine gap penalty and evaluate the probability that the two (2) aligned sequences share the same structural fold.

Build multiple sequence alignments, construct and plot evolutionary trees, visualize sequence clustering in two (2) and three (3) dimensions, and predict protein secondary structure with a set of advanced algorithms.

Search your sequence interactively or via batch through any database and generate a list of possible homologues that are sorted and evaluated by the probability of structural significance. The sensitive and rigorous Zega alignment is used for each comparison.

This search may give you more homologues than a BLAST search! The output can be presented in a linked table form. The text sequence databases can be indexed and queried with ICM.

Key Bioinformatics Features include:

Sequence Analysis, Sequence Alignments, Multiple Sequence Alignments, and Sequence Search.

ICM-REBEL Electrostatics -- Use ICM-REBEL to calculate the accurate electrostatic potential of a molecule using the boundary element algorithm and generate a 3D surface skin model colored by potential.

ICM-REBEL - The ICM-REBEL module allows you to solve the Poisson equation for a molecule without a grid and with exact positions of electric charges. REBEL is a new advanced implementation of the boundary element method with analytical molecular surface as a dielectric boundary. This method is fast (takes seconds for a protein) and accurate.

REBEL stands for (Rapid Exact-Boundary ELectrostatics). The energy calculated by this method consists of the intramolecular Coulomb energy and the solvation energy which can be analyzed separately.

With REBEL, you can easily and quickly calculate and evaluate the following:

Electrostatics - Evaluate separate components of the electrostatic free energy. Use these energies in the structure prediction by global energy optimization in a double energy scheme.

Color by Potential - This REBEL feature calculates the electrostatic potential away from the surface of the graphics object and colors surface elements according to this potential from red to blue. The potential is calculated either by the REBEL boundary element solution of the Poisson equation, or, if the ‘fast option’ is specified, by a simple Coulomb formula.

Drug Binding Energy - Used in conjunction with the electrostatic solvation component, ICM-REBEL allows you to determine the specific energy for binding. This includes the ability to determine the electrostatic component of drug-receptor binding activity.

Maps - Allows you to map the electrostatic potential and its isopotential contours for an accurate and detailed representation of your model. ICM-Rebel is included in the ICM-Pro package.

Chemistry Tools -- A variety of chemistry tools are available. Chemicals can be sketched in the ICM Molecular Editor and viewed in a chemical spreadsheet. Additional chemistry tools are available in ICM-Chemist and ICM-Chemist-Pro (additional software products).

Molecular Graphics -- Utilize a full and robust array of graphics tools all accessible from a GUI interface. Display your molecules in wire, CPK, ball & stick, worm, ribbon, accessible surface, transparent molecular surface, perspective, depth cueing, smooth and rugged solid surfaces.

Use both hardware and side-by-side stereo. Save and print a screen image as a compact vectorized postscript file (also in stereo) in addition to a compressed bitmap.

Painlessly create movies featuring molecules dressed in solid representations such as CPK, smooth molecular surface, ball-and-stick read, display, reshape and write any 3D object in the Wavefront format.

Key molecular graphics Features include:

Export publication quality molecular images at high resolution and vector images (metafile); Annotate, atoms, residues and sites;

2D and 3D user-defined labels; Hydrogen bond and distance labels; Display atom clashes, distance restraints, and tethers;

High quality molecular surface representation, skin, wire, xstick and ribbon representations;

It provides easy control of thickness, color, and type in molecular graphics; Color by atom type, residue side-chain, molecule, unique carbon atom coloring for multiple objects, B-factor, occupancy, accessibility, hydrophobicity, polarity, secondary structure, paint structure by alignment color, and color by user-defined values;

Visual effects: dynamic shadows, fog, hardware and side-by-side stereo, clipping planes, full screen; Export colored and annotated sequence alignments; Easy to use and control animation effects: rotations, rocking, zooming;

Store current views/viewpoints, layers and slides; Two kinds of stereo, including a high quality “in-window” mode, as well as a stereo mode which does Not require any special hardware.

System Requirements

Available Platforms: Windows 7/Vista/XP/NT/2000, Linux/i386/AMD64, SGI IRIX, Mac OS X and contact manufacturer for Minimum Specifications.

Manufacturer

Manufacturer Web Site ICM-Pro

Price Contact manufacturer.

G6G Abstract Number 20720

G6G Manufacturer Number 104290