ICM-Pro empowers a biologist or chemist by providing a high quality protein structure analysis, modeling, and docking desktop software environment. You have direct access to sequence and structural databases which allows you to: analyze sequences and alignments, inspect protein structure, study pockets and bound ligands and drugs, create surfaces, calculate electrostatics, make mutations, predict ligand binding sites, predict protein-protein interaction sites, perform small molecule and protein-protein docking and design ligands using the Interactive Ligand Editor.
Features
ICM-Pro empowers a biologist or chemist by providing a high quality protein structure analysis, modeling, and docking desktop software environment. You have direct access to sequence and structural databases which allows you to: analyze sequences and alignments, inspect protein structure, study pockets and bound ligands and drugs, create surfaces, calculate electrostatics, make mutations, predict ligand binding sites, predict protein-protein interaction sites, perform small molecule and protein-protein docking and design ligands using the Interactive Ligand Editor.
Protein Structure Analysis. ICM-Pro provides a direct link to the Protein Data Bank (PDB). Once you have downloaded a structure you can analyse the structure - build Ramachandran plots, superimpose multiple structures, analyse distances and angles, calculate contact and surface areas, display hydrogen bonds, build electrostatic surfaces and calculate ligand binding pockets.
ICM 3D Interactive Editor. Interactively edit a chemical inside a receptor binding pocket. Modify atoms and groups and see the effect of the changes on ligand binding energy and score. Re-dock and minimize ligand...
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 you may want to contour the electron density to see how much of a ligand was seen by the crystallographer in the active site.
Small Molecule Docking. ICM-Pro provides a unique set of tools for the modeling of protein/ligand interactions. ICM-Pro performs fast and accurate docking of fully continuously flexible small molecule ligands to a protein represented by grid interaction potentials. There are also inbuilt procedures to account for induced fit which include multiple receptor docking (4D docking) and explicit receptor docking.
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.
Protein Structure Prediction. ICM-Pro has a good record in protein modeling. There are procedures which will regularize or build the backbone, shake up the side-chains and loops by global energy optimization. You can also perform simulations of small peptide folding.
Bioinformatics Tools. The ICM-Pro package contains all the tools in ICM-Bio which allows you to search a sequence database with high-quality global pairwise and multiple alignment algorithms and perform pattern, prosite and profile searches. Multiple sequence alignments are fast, the algorithm produces evolutionary trees, principal component views, annotation transfer from sequence to structures, threading and alignment visualization tools.
Electrostatics. The Poisson equation for a molecule of any size can be efficiently solved using the boundary element algorithm that does not depend on any grid, and uses the exact analytical molecular surface as the boundary. ICM-REBEL calculates the accurate electrostatic potential of a molecule using boundary element algorithm and generates a 3D surface skin model colored by potential.Solves the Poisson equation for a molecule with exact positions of electric charges.
Chemistry Tools. A variety of chemistry tools are available. Chemicals can be sketched in the ICM Molecular Editor and viewed in a chemical spreadsheet.
Molecular Graphics.ICM-Pro contains all the tools in ICM-Browser-Pro 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, side-by-side, and Anaglyph stereo.
http://www.molsoft.com/icm_pro.html
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