Markush Tools

A Toolkit for the analysis of virtual combinatorial libraries and patent Markush structures

Markush or generic structures are widely used in combinatorial libraries and chemical patents to define large chemical spaces. ChemAxon provides the most advanced Markush technology, including rapid structure searches in Markush space, enumeration, overlap analysis - including automatic Markush composition. Markush analysis features are available as add-ons for many ChemAxon products, like JChem Engines and Instant JChem.
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Markush representation

Markush representation supports all important structure variations, and even enables advanced Markush features to handle combinatorial virtual libraries and complex patent Markush structures. ChemAxon’s .mrv file format fully supports all current Markush features. Highlighted features that the technology can handle:

  • Atom and bond lists
  • Position variation bonds
  • Link nodes
  • Repetition units
  • Multiply connected R-groups
  • Heavily nested R-groups
  • R-group bridges
  • Homology groups

Markush generation

A Markush structure can be generated automatically using R-group decomposition or Markush Composer. R-group decomposition identifies all R-group substituents, starting with a structure library and defining a common scaffold. Using these substituents an R-table or a Markush structure can be created. Markush Composer can calculate optimal scaffold automatically, and it can generate simple combinatorial, or complex patent Markush structures. A created Markush structure covers all possible combinations of starting compounds. Generated Markush structures can be ideal starting points to finding new potentially effective compounds or for creating your own patent Markush structure.

Composing Markush structures with Markush Composer

Markush enumeration

Markush Enumeration is a robust tool for Markush structure analysis. By interactively guiding each Markush enumeration structure, users can quickly identify the relevant Markush that suits their needs. Current enumeration types include:

  • Full, partial, and random enumeration
  • Library size calculation
  • Homology enumeration

Markush Overlap analysis

Markush Overlap analysis is a powerful automatic analysis technology for comparing two Markush structures. It's capable of calculating overlapping chemical spaces between two Markush compounds - regardless of molecule complexity. The percentage of overlap, and the Markush representation within the overlapping chemical space is calculated.

Markush overlap analysis

Markush non-hit visualizations

Markush non-hit visualization is a visual analysis technology for comparing a Markush structure and a compound. It can highlight both the matching and non-matching parts in a query structure and in R-groups of a target Markush structure. The differentiating parts can be easily recognized and analyzed in this way.

Markush non-hit visualization