ChemAxon: Revolutionizing Generic Chemical Structure Searches

[tweetmeme source=”Intellogist” only_single=false] Searching for Markush structures is a difficult task, and professional searchers need training and experience to search competently for Markush structures in the MMS database.  Markush structures originate in patent claims (Markush claims) for generic chemical compounds, and a single Markush structure could correspond to thousands of different specific chemical structures (enumerations).  The Merged Markush Service (MMS) was created in 1998, after the merger of two generic structure databases owned by Thomson Derwent and the French Patent Office (INPI).  Until recently, the MMS file was only accessible via the Questel Imagination platform or the STN Express platform, and both platforms require command line searching in order to draw, search, and display structures.  The chemical drawing tool Topfrag is available through Questel, but this program must be purchased.

Luckily, users now have a third option for searching MMS: through JChem  and MarvinSketch, created by  ChemAxon.  Thomson Reuters recently partnered with ChemAxon to make Markush DARC (MMS) records available on the JChem platform.  Continue reading to discover the unique search, display, and analytic capabilities of ChemAxon products!

Structure Drawing on MarvinSketch

Chemical structures in JChem can be drawn using MarvinSketch, the “integrated structure drawing tool of JChem.”  The MarvinSketch user guide gives detailed instructions on how to utilize all features of the program, including how to draw Markush structures and R-group queries with the software.  The MarvinSketch structure drawings can be uploaded directly to the query form, and users can also select Markush structures from the results list  in order to edit the selected structure and create a new query.

Users can draw and edit Markush structures in the MarvinSketch chemical drawing tool.

Searching on JChem

Once the user has uploaded a saved structure drawing from MarvinSketch into the query form, they can define the type of search they wish to conduct (Duplicate, Substructure, Superstructure, Full and Full-Fragment search types).  Users also define other attributes of the structure query (stereo-chemistry, atom matching, etc.) and add any additional limiting criteria or text terms.  Once a user has selected the options to apply to the structure query and added any additional text terms, they can run the query in the MMS database.

In JChem, a user can first view the search result “hit list” for Markush structures in the window to the right of the query form. The list can either be in Grid view (which resembles an Excel spreadsheet) or Form view, which is shown in the image below.  In the Form view of the Markush hit list, the list of Markush structures is displayed next to the specific bibliographic data for the currently selected search result. The list displays an image of the Markush structure and a count of the number of possible enumerations for the structure.

The query and search results for a Markush structure search in Instant JChem.

Users can also select to view the relevant R-groups in the search results that correspond with the R-groups in the search query.

A focused view of the relevant R-groups for a Markush structure search result.

Enumeration and Analysis

From the Markush structure hit list, users can select to view the enumerations (specific chemical structures) that correspond with the selected Markush structure.  Select the “colouring” option to highlight the relevant R-groups in the enumerations.

When viewing structure enumerations, users can highlight the relevant R-groups.

In the menu of enumerated results according to a single Markush structure, users can also select “Markush reduction according to the hit” in order to only view enumerations that match the original structure query.

Users can analyze the list of enumerations by selecting the “Filter” tab in the enumerated structure menu.  In the “Chemical terms filter” editor, predefined chemical term filters listed under the “Favourites” drop-down menu are available.  Users can also manually enter their own chemical term expressions into the editor form.  Suggested chemical terms will automatically appear as the user types.  After defining the relevant chemical filter, users select “OK” in the editor form to filter the list of enumerations.

Filter the enumerations by user-defined chemical terms.


ChemAxon’s chemical drawing tool, query form, hit list, and structure display features all are far easier to use than Questel’s or STN’s command-based platforms.  However, users should still carefully read all help guides for the JChem system, so they will know how to properly utilize its revolutionary features like Markush enumeration, hit reduction, and chemical filtering.  The main problem with JChem is that it isn’t directly linked to the MMS file, so users must purchase access to the MMS file separately and manually upload or link the MMS records to the JChem platform.  Hopefully JChem will eventually become a hosted online service with direct access to the MMS file through a single log-in.

Have you used JChem or any other ChemAxon product for generic chemical structure searches?  How was your experience with the product?  We’d love to hear your opinion in the comments!


PostscriptAccording to Szabolcs Csepregi, PhD, the Director of Search Technologies and Markush Project at ChemAxon, the current workflow of the JChem platform allows in-house searching of the MMS file and also handles search and analysis of the user’s own Markush structures.  This workflow wasn’t possible with the previous online tools, and some users may prefer this process because of the amount of privacy it offers.  ChemAxon provides support for loading the files on the customer’s hardware in consultancy, and ChemAxom consultants can also help with setting up virtual servers.

Patent Analysis from Landon IP

This post was contributed by Joelle Mornini. The Intellogist blog is provided for free by Intellogist’s parent company Landon IP, a major provider of patent searches, trademark searches, technical translations, and information retrieval services.


2 Responses

  1. An additional important feature of Instant JChem makes it invaluable to those doing computational or medicinal chemistry. When developing a product like a new medicine, many structures may be developed in silico, but third party patents may not allow for those compounds to be commercially developed. To help find products that are not blocked by patents, large numbers of candidate structures can be imported automatically and searched against DWPI Markush data using Instant JChem to allow quick determination of which are covered by existing patents. Once the specific and Markush chemical structures and the patents that contain them are identified, the structures may be analyzed by ChemAxon property predictions or exported electronically to other computational chemistry software for further property prediction. We expect that this will be another major use for this invaluable tool, which will provide critical information early enough in the product development process to avoid costly investment in products that are not commercially viable.
    Donald Walter
    Thomson Reuters
    Product Specialist

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