ICM-Chemistry

ICM-Chemistry provides a rich cheminformatics environment allowing you to build, view and manipulate chemical structures. This product seamlessly interacts with the ICM-Pro graphical user interface and command line allowing you to link biological structures with chemistry functions. These tools are ideal for structure-based or ligand-based virtual screening experiments and lead optimization projects. A useful companion to ICM-Chemistry is MolCart and MolCart Compounds.

Some of the key features of ICM-Chemistry are described below:

Chemical Drawing

• Draw compounds using an easy-to-use molecular editor
• Keyboard shortcuts for fast molecule sketching
• Large selection of annotated templates
• Full support for smiles and smarts including annotation and dynamic highlighting of functional groups
• Automated 2D drawing from 0D or 3D sdf files
• Draw compounds whilst monitoring key properties (eg Log P, drug-likeness etc..)
• Save files in mol, sdf and smiles format

Chemical Display

• Generate, manipulate, annotate and display chemical spreadsheets
• 3D compound browsing in graphical display
• "Browse and Lock" chemicals in graphical display
• Highlight substructure in chemical spreadsheets
• Color by properties
• Select and mark compounds

Structural Chemistry

• Convert chemicals to 3D using the Merck Molecular Force Field (MMFF)
• Generate stereoisomers and tautomers
• Generate chemical conformations
• Easy modification of a ligand in a 3D protein structure.
• Chemical superposition - rigid, flexible, template based, and, multiple chemical property alignment
• All functions can be performed interactively or in batch mode

Chemical Searching - Ligand Based Screening

• Chemical similarity searching - substructure, fingerprint similarity, atom and bond properties (Smiles and Smarts), search patterns (terminating and hybridization), and, exact match
• Search local tables (SDF, Mol Files) or MolCart
• Pharmacophore searching in conformer databases or files
• 2D and 3D pharmacophore searching in compound databases
• Pharmacophore editing tools in 3D and 2D

Library Generation

• Virtual chemistry library generation using reactions
• Markush based library generation with on the fly filters
• Split into fragments to generate a series of R groups.
• Find and replace chemical editing e.g. (C(=O)O to C(=O)OC)
• Fragment generation by rotatable bonds and Markush scaffold
• Focused library generation
• Compare chemical tables (sdf files)
• Structure-based and ligand-based virtual screening

Chemical clustering

• Hierarchical clustering and trees
• Various methods for selecting a subset of representative structures
• Fast chemical clustering with a variety of Linkage Types
• Extract representative "center" structures from each node.
• Branch reordering and distance changing

QSAR

• Predict compound properties - LogP, LogS, PSA, hERG, aggregation, CYP3A4, druglikeness, reactive chemical groups, Heats of Formation, Lipinski, etc..
• Various methods for linear and non-linear QSAR including, both regression and classification methods
• Machine learning tools for regression or classification with the following kernels radial, scalar products, polynomial, sigmoid and tanimoto
• Cross validation and boot-strapping
• Save models and data plotting