Skip to main content
  • Oral presentation
  • Open access
  • Published:

Representation of Markush structures: from molecules toward patents

Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent applications for the description of compound classes.

The presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and larger repeating units, position and homology variation). Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space is searchable without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and their enumerated libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).

Special attention will be given to file formats and how they were extended to hold generic features.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Szabolcs Csepregi.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Csepregi, S., Máté, N., Wágner, R. et al. Representation of Markush structures: from molecules toward patents. J Cheminform 3 (Suppl 1), O7 (2011).

Download citation

  • Published:

  • DOI: