Markush Technology

Toolkit for the analysis of virtual combinatorial library and patent Markush structures

Markush structures, 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 search in Markush space, enumeration, overlap analyses, and automatic Markush composition. All Markush analysis features are available as an add-on for ChemAxon’s JChem technology (JChem Base, JChem Cartridge and Instant JChem).

Product Type:component
Interfaces:CLIAPI ( Java, .NET )

ChemAxon’s solution for handling Markush structures

Markush representation

ChemAxon’s market-leader Markush representation supports all important structure variations to be able to handle combinatorial virtual libraries and complex Patent Markush structures, such as atom lists, bond lists, position variation bonds, link nodes and repetition units. Advanced Markush features, such as multiply-connected R-groups, heavily nested R-groups, R-group bridges and homology groups are also supported. ChemAxon’s .mrv file format fully supports all current Markush features.

Markush structures

Markush drawing

Marvin and Marvin JS as general drawing tools are perfect for handling smaller Markush structures but not for structures with hundreds of fragments. Markush Editor is designed for creation and visualization of complex combinatorial and patent Markush structures. With built in Composer wizard you can generate Markush structures automatically and by validation, enumeration, hit and non-hit visualization you can analyze them easily.


Markush generation

Besides drawing it manually, a Markush structure can also be generated automatically using R-group decomposition or Markush Composer. R-group decomposition identifies all R-group substituents, starting with a structure library and the definition of the common scaffold. Using these substituents an R-table or a Markush structure can be created. Markush Composer can calculate the optimal scaffold automatically and it can generate combinatorial, and also complex patent Markush structures. The created Markush structure, covering all possible combinations of your starting compounds, can be ideal starting point to generate new ideas or create your own patent Markush structure.

Markush Structure Generation

Markush Enumeration

Markush Enumeration is a powerful tool for Markush structure analysis and is fully implemented in JChem. By interactively guiding the enumeration of the Markush Structure users can quickly understand the relevance of Markush to their needs. Current enumeration types include; full, partial, and random enumeration; library size calculation; homology enumeration.

Markush Enumeration

Markush Overlap analysis

Markush Overlap analysis is a powerful automatic analysis technology to compare two Markush structures. Capable to calculate the overlapping chemical space between two Markush compounds regardless of the complexity of the molecules. The percentage of overlap and the Markush representation of the overlapping chemical space can be calculated.

Markush Overlap analysis

Markush Non-hit visualization

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

Markush non-hit visualization

ChemAxon’s Markush Search

Searching in Markush spaces

Markush Search is a powerful tool for structure search in a large chemical space defined by a generic Markush structure, without actually enumerating the explicit compounds. This approach enables the exploration of extremely large Markush spaces, which would be unthinkable by traditional search techniques. In case of multiple substructure queries against a library of Markush structures, an “Overlap Analysis” can be applied, returning the hits for each query structure separately. ChemAxon’s Markush technology now allows users to submit Markush structures of limited complexity as a query. Query Markush structures can contain the same Markush features that can be present in general Markush structures, which makes the comparison of simple Markush spaces possible.

Markush Searching

Rich visualization features

Hit coloring and automatic structure alignment make the visualization of the search results easier. The features for better visualization include 2D-cleaning for the hit structures. Users may also choose to reduce visualization on the Markush core only. Alternatively, non-relevant R-groups can be filtered out to display only essential information or all R-groups can be shown. For an even “cleaner” display, Markush Reduction can be applied.

Markush relevant R-groups

Markush structures in a workflow

Markush Code GenerationWorkflow management solutions play a more and more important role in everyday research processes. ChemAxon’s Markush analysis plug-in is implemented in KNIME and in Pipeline Pilot, two commonly used workflow management tool-kits. These implementations includes Markush Search, Markush Enumeration, and Markush structure generation which makes this technology easily accessible and integratable into best practice routines.

Articles in the library

AMRI Leverages Instant JChem for Compound Libraries

Sep 15, 2016 - Presentation
AMRI recently launched a Compound Library Consortium (CLC), to deliver 70,000 compounds within 2.5 years for three different partners. AMRI selected Instant JChem (IJC) from ChemAxon to …

Merck Virtual Library (MVL): Deployment, Application and Future Enhancement

Sep 14, 2016 - Presentation
An update of MVL will be given with some observations obtained from its one-year long cloud deployment in terms of performance, robustness, cost, and admin effort required. An overview of…
Author: ()


May 24, 2016 - Presentation
ChemCurator is a desktop application to extract chemical information including compounds, Markush structures and related assay data from English, Chinese and Japanese patents, journal art…

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