ICM-Chemist

ICM-Chemist is a standalone suite of programs developed by Molsoft L.L.C., designed for medicinal chemists and cheminformatics professionals working with chemical drawing, database generation, searching, clustering, and library enumeration. It combines a rich set of 2D and 3D chemical analysis tools into a single environment, making it suitable for drug discovery teams who need to manage and interrogate large chemical datasets efficiently. ICM-Chemist also includes all tools found within ICM Browser Pro, and users requiring additional 3D capabilities, chemical superposition, interactive ligand-receptor editing, and QSAR model building can upgrade to ICM Chemist Pro.

The platform supports the full lifecycle of small-molecule research, from initial compound sketching and property monitoring through to combinatorial library generation, pharmacophore searching, and structure-activity relationship analysis. QSAR prediction models built in ICM-Chemist Pro can also be read in and applied directly within ICM-Chemist.

Chemical Drawing and Editing

• The ICM Molecular Editor provides an easy-to-use chemical sketch pad for fast and accurate chemical structure drawing.
• Drug-like properties and potentially toxic groups can be monitored in real time as structures are sketched.
• A built-in database of substructure templates and a chemical dictionary support rapid structure entry.

Chemical Database and Spreadsheet Capabilities

• Chemical spreadsheets provide a rich environment for displaying and manipulating chemical datasets.
• Large chemical libraries containing millions of compounds can be stored in fully optimised local databases for fast search and operations such as unique entry addition and diverse subset selection.
• Databases can be created from SDF, CSV/TSV, SMILES, and chemical spreadsheet formats.
• A wide variety of chemical and mathematical functions can be applied to spreadsheets or local databases, including on-the-fly property calculation, arithmetic, transformation, and unit conversion.

Chemical Searching and Filtering

• Search chemical databases using substructure, pattern, fingerprint similarity, and exact match methods.
• Many customisable search rules and filter types are available to refine results.
• 2D and 3D pharmacophore searching allows users to sketch and edit pharmacophores and search compound database files, with hits scored and displayed in a chemical spreadsheet.

Property Calculation and Multi-Parameter Optimisation

• A wide range of ADME properties can be rapidly and accurately calculated across large chemical datasets.
• Chemicals with potentially poor ADME-TOX profiles can be flagged prior to experimental testing.
• Multi-Parameter Optimisation (MPO) enables users to derive composite scores reflecting the relative importance of multiple chemical properties.
• Built-in MPO scoring schemes include CNS, Lipinski Rules, and Quantitative Estimate of DrugLikeness (QED).
• Users can also create custom MPO scoring schemes tailored to their own project requirements.

Structure-Activity Relationship and Clustering Analysis

• SAR tables, plots, and activity cliff analysis can be generated to support lead optimisation.
• Hierarchical chemical clustering and tree visualisation are available using Tanimoto distance and a variety of other data types.
• Cluster trees support fully interactive branch reordering and distance adjustment, with the chemical spreadsheet coloured by branch and representative cluster centres selectable.

Library Enumeration and Stereoisomer Generation

• Combinatorial chemical libraries can be generated by creating or modifying Markush structures and enumerating on the fly by adding chemical fragments to defined R-groups.
• Enumeration by chemical reaction and decomposition of databases into chemical fragments are also supported.
• Stereoisomers and tautomers can be generated in batch mode or interactively from a table, mol, or SDF file.
• Undefined R/S forms can be enumerated or converted to racemic for chiral compounds.

Visualisation and Interaction Diagrams

• 2D ligand-receptor interaction diagrams can be generated, annotated with hydrogen bonds and interacting residues.
• Residue interaction surface and proximity are represented visually by label size and distance, with solvent-accessible regions and ligand property shading included.
• Interactive plotting tools include histograms and X-Y scatter plots, with 2D, 3D, 4D, and 5D plotting options available.
• Selections made in plots are directly linked to the chemical spreadsheet for seamless data exploration.
• Plots can be printed or exported as images.

File Format Support

• Chemical data can be imported and saved in SDF, mol, SMILES, reaction, and CSV formats.
• Files can be exchanged between ICM-Chemist and ISIS Draw.

ICM-Chemist is available as a standalone desktop application, and Molsoft provides minimum recommended hardware specifications to ensure optimal performance. The platform is well suited to medicinal chemistry and cheminformatics workflows in pharmaceutical and biotechnology organisations.