Creating and understanding Markush libraries: Markush Editor

Posted by
Árpád Figyelmesi
on 03 09 2014

Markush structures are widely used in combinatorial chemistry and patents to define large chemical spaces. However, handling complex Markush structures (containing hundreds of fragments) with existing structure editors, including Marvin, is extremely challenging.

While ChemAxon already has a useful technology in our Markush Viewer, the technology base is old and not a good starting point to add the extensive editing capabilities we were thinking of. We also wanted to include some of our Markush search/canonicalisation tech, in the background to make the editor chemically and Markush ‘aware’. So we started from scratch revisiting the topic with completely fresh eyes, a strong image of where we want to go and a fair list of use cases to base our works on.

We hope you agree that Markush Editor will be a valuable tool for IP experts and chemists to draw and edit complex markush structures faster and with more confidence than ever before.

Major usability features:

1 Hierarchical representation of fragments’ relationships 2 Simple editing of individual fragments 3 Visualization of R-group nesting as well as color coded previews of enumerated structures 4 Integrated Structure Checker to automatically identify and fix errors, specifically around common Markush structure errors

Have a look at this 1 minute video creating a simple Markush with 3 R-groups and nesting in Markush Editor.

Register for free webinar

Arpad Figyelmesi, former patent examiner and project owner for ChemAxon’s Markush developments is introducing Markush Editor on 25th June at 4pm CEST, to join us register at this link.

How can I get it

Markush Editor is available as a desktop application, you can download the installer from the product information page. It can be used as a viewer without a license but is unable to create and edit. You can create a 3 day evaluation license automatically, you need to be registered and logged in to access.

Markush Editor can also be integrated in your own application as a component from the JChem API. Contact us for an evaluation license to enable.


Markush Editor in 6.3 is only the first stage of a longer term development. Already Markus Editor is integrated with a new product (ChemCurator) being launched later in the summer, see a poster covering the functionality. We are also planning to make Markush editing available in Instant JChem and we hope to have that available still this year.