MedChem Studio™

Advanced data mining and molecule design

Choose a Module:

Basic Module

What is the Basic Module?

MedChem Studio’s Basic Module allows one to perform class generation.  This technology reproduces the chemist’s reasoning by automatically organizing molecules into chemical families based on shared scaffolds:

  • “Frameworks” class generation option similar to the Murcko assemblies method
  • Uses maximum common substructures (MCSs) rather than fingerprints, so results are chemically intuitive
  • Learns scaffolds from the data rather than reading them from a pre-defined list, so novel structural motifs can be discovered
  • Provides an ideal starting point for local QSAR generation, molecule design, and other analysis tasks


Effortless R Table Generation & R Group Analyzer

MedChem Studio can build R tables using only a molecule list as input:

  • Scaffolds and R groups are determined automatically
  • You can extract SAR by isolating molecules that differ at only a single specified R group
  • Each fully customizable table can be exported to Excel or other software application
  • R group columns can be sorted for easier SAR detection
  • R group pairs allows you to analyze your chemical data by visualizing the effects of various substitutions on molecule properties

R Group Analyzer

With this tool, you can convert a traditional R table spreadsheet into one that shows unique substituents at each R position along with the average substituent properties (e.g., activity, logP, etc…) and distribution charts.


MedChem Studio contains a powerful and robust query language that offers multiple options for selecting molecules containing specific molecular features and/or properties:

  • Substructure queries can be sketched using the integrated MedChem Designer™ software
  • Property queries can be encoded with our easy-to-use Query Wizard
  • Use the internal list of special named queries (e.g., aromatic ring count, atom count, or largest ring size)
  • Queries can be easily combined using logical operators

Similarity Searching and Diversity Selection

MedChem Studio easily performs similarity searching or diversity selection:

  • Similarity searching allows you to find molecules similar to a query molecule to help expand your SAR
  • Calculate similarities using molecules in the open document or an external file
  • Customize scores by modifying the similarity metric (e.g., Tanimoto, Euclidean, or shared keys) or fingerprint type
  • Diversity selection can be utilized to find suitable screening compounds from a large library

Benefit from these additional Basic Module features:

  • Structure Standardization
    • “Clean up” structures so that they are represented in a consistent manner:
      • Generate and export Kekule SMILES strings
      • Counterions and salts can be removed from multi-component molecules
      • Generate canonical SMILES strings
  • Convert file formats (e.g., SMILES to SD)
  • Filtering
  • Maximum Common Substructures
  • 2D Coordinate Generation
  • Command Line Option
  • Pipeline Pilot™ Integration
  • Add comments and export with various files
  • … and more!