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Markush Enumeration

webinar · 10 years ago

Markush Enumeration

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A Markush structure is a description of a compound class by generic notations, primarily used in patent claims and the description of combinatorial libraries. The library of a Markush structure is the total set of specific molecules that are described by the Markush structure.

The Markush enumeration plugin can be used to generate a whole or a subset of the library of a generic Markush structure. It is also capable of calculating the total number of specific structures present in a Markush library.

The plugin handles the following Markush features: R-groups, atom and bond lists, link nodes, repeating units, position variation bonds and homology variation.

Markush Search

Markush Search is an add-on to JChem Base and Instant JChem and allows the registration of generic structures into the database as well as substructure and full structure searching in their enumerated libraries (without enumeration of library members). More information.

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What is Markush Enumeration?
Markush Enumeration is a calculator plugin that is able to enumerate Markush structures to specific structures.
What is Markush Enumeration good for?
It can enumerate specific structures contained in the Markush library of a Markush structure. The plugin supports coloring and alignment of specific structures to help better associate them to the original Markush structure, and provides full, selective and random enumeration.
Do I have to do programming for using Markush Enumeration?
Not necessarily. Several GUI-s are available:
  • plugin interface in Marvin Sketch and View
  • Instant JChem: Enumeration dialog for Markush tables
  • JSP web example of JCB offers a simple example Markush enumeration web page.
Other interfaces include:
  • API
  • command-line: cxcalc
  • JChem Cartridge (via Chemical Terms)
What Markush features are supported?
The following generic features are currently supported:
  • R-groups (nested to any depth)
  • atom and bond lists
  • link nodes and repeating units
  • position variation bonds
  • homology variation (predefined generic atoms - alkyl, aryl, etc. and user-defined ones, like protecting group)
How can we identify which part of an enumerated structure comes from which R-group, etc?
The Markush enumeration plugin helps in numerous ways:
  • R-group coloring: the scaffold and all top-level R-groups are coloured differently.
  • The scaffold is oriented the same way as in the Markush structure.
  • A Markush code (enumeration ID) can describe which definition was used for the enumeration of each library members.
Where can the Markush structures come from?
  1. Combinatorial:
    • Molconvert+Reactor+Standardizer can produce R-group definitions from reagent sdf files.
    • A Markush Rgfile output is under development in libMCS.
  2. Patent:
    • In-house Markush data can be curated using MarvinSketch.
    • We plan to implement common Markush file formats. (e.g. Markush DARC used by MMS)