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Contents

Introduction

ChemAxon is the producer of software development platforms and desktop applications for biotechnology, pharmaceutical, agrochemical research, publishing and intellectual property analysis. The company focuses on structure visualization, search and management, property prediction, virtual synthesis, screening and drug design technologies.

ChemAxon now supports Markush DARC indexing available in the Merged Markush Service (MMS) database from Thomson Reuters. This allows existing cheminformatics and other techniques to be applied to explore and visualize Markush libraries. The Markush DARC files are supported on ChemAxon's JChem platform.

At this time ChemAxon's Markush search technology will perform a comprehensive structure search against Markush libraries (without enumeration) and enumerate partial or complete libraries to obtain final chemical structures that can be exported for further analysis.


Major Recent Updates

In March 2012, JChem and Marvin 5.9 were released. See a summary of the latest features for JChem here and new features for MarvinSketch here.

In January 2012, JChem and Marvin 5.8 were released. See a summary of new features for JChem 5.8 here and new features for Marvin 5.8 here.

In November 2011, JChem and Marvin 5.7 were released. See a summary of new features for JChem 5.7 here and new features for Marvin 5.7 here.

In September 2011, JChem and Marvin 5.6 were released. See a summary of new features for JChem 5.6 here and new features for Marvin 5.6 here.

In May 2011, ChemAxon released JChem and Marvin 5.5.[1] Major changes and features to Marvin 5.5 include:[1]

  • Bold Tool thickens molecular bonds to improve visualizing the perspective
  • Improved display of aromatic rings in 3D
  • Sketch canvas can be scrolled by arrow keys, zoomed using the mouse wheel
  • Inserting special characters and symbols within reactions
  • Marvin can differentiate syn, anti, endo, exo, allene, cumulene, atrop and other axial stereo isomers at API level; and export syn, anti, endo and exo into ChemAxon
  • Extended SMILES and SMARTS formats
  • Electron flow arrows are redesigned
  • Java 1.6 is required
  • Substructure Checker: detects user defined substructures (requires JChem)
  • Major rewrite of the Name to Structure converter. Higher precision (around 50% improvement) and support for additional names

Updates in JChem 5.5 include:[1]

  • Sophisticated formula search in JChem Base and Cartridge
  • New stereo types support in structure searching: syn, anti, atrop, allene, cumulene
  • Search performance enhancements: R-group search and database Markush search
  • Support for large Markush structures (up to thousands of R-group definitions)
  • Reactor supports copying reactant fields to products
  • Substructure Checker: allows the specification of custom checkers in SMARTS format
  • Manual selection of preferred regioisomeric products in Reactor
  • ECFC: ECFP now supports feature frequency counts
  • ECFP: feature lookup is available (fingerprint ‘bit’ can be traced back to relevant substructure)


In April 2011, ChemAxon announced "the release of JChem for SharePoint to fully enable chemistry within Microsoft’s SharePoint™ platform. The launch includes Web Parts and Custom Lists for chemical editing, search and property prediction."[2]

In January 2011, Thomson Reuters and ChemAxon announced that Thomson Reuters chemical IP Data Feeds (Markush Structures and patent data) would be made available to ChemAxon's JChem chemical software platform.[3]

In November 2010 Gridlogics, the producer of the patent analysis tool Patent iNSIGHT Pro, announced that they had partnered with ChemAxon to produce a version of Patent iNSIGHT Pro specifically for the chemistry and bio-pharmaceutical industries. This new product is known as the CHEMPAT™ Edition.

The CHEMPAT Edition product will analyze patent data to extract chemical names automatically, and the data may then be analyzed using Patent iNSIGHT Pro technology.

A full description of the CHEMPAT product is available from the November 2010 PIUG wiki post announcing its introduction here.


ChemAxon Technologies Relevant to the IP Field

Desktop applications (all major platforms)

  • MarvinSketch for editing and viewing chemical (including Markush) structures, reactions and queries.
  • Instant JChem for structural and non structural database management and search. Including support for Markush search and review of entire MMS data library.
  • Calculator Plugins for prediction of various properties based on structure (pKa, logP, charge, name to structure, conformers, Markush enumeration, etc). Can be applied to profile Markush structures or filter enumerates.
  • JChem for Excel - Enables chemistry in MS Excel, Markush structures supported.
  • JChem for SharePoint - Search and manage chemical structures in SharePoint.

Platform IT toolkit (all major platforms and database engines)

  • JChem Base for chemical and Markush structure and reaction searching and database handling.
  • JChem Cartridge for Oracle® database integration.
  • Standardizer for structure canonicalization.
  • Structure Checker for batch structure file validation and correction.
  • Markush Search - Add on: Store & search Markush structures, as well as substructure and full structure searching in their enumerated libraries (without enumeration of library members).
  • JChem Web Services - Add on: Web services integration interface.


Markush Structure Searching in JChem

Installing JChem and Linking to MMS

Users can purchase the software Instant JChem, which is "a desktop application for end user scientists" created by ChemAxon.[4] The latest version of Instant JChem, version 5.5.0, contains the following components:[4]

  • Instant JChem
  • Name to Structure
  • JChem Base
  • Markush Search
  • Standardizer
  • Calculator Plugins
  • Reactor

Users must make sure that they already have full access to the MMS database through another server, since ChemAxon does not provide the MMS files with the JChem software. After downloading the software, users should start JChemManager, which is a "tool for creating and deleting structure tables and importing and exporting structure files into and out of these tables."[5] The "Administration Guide of JChem" gives detailed instructions on Installing and Starting JChemManager.


Use JChemManager to connect to a database (image from JChem User Guide).


Information on the import and conversion of Markush DARC (*.vmn) files can be found here on the ChemAxon website. According to this guide:[6]

Thomson Reuters Markush DARC (*.vmn) files contain Markush structures extracted from patents. This is the "Merged Markush Service database", now owned and distributed by Thomson Reuters. These files are particularly useful when imported into a JChem table of type Markush libraries as you can search the table of Markush structures using substructure or exact structure searches.

After using JChemManager to import the database files of MMS, users can create a new project in Instant JChem.


Searching for Markush Structures in JChem

After a user has linked the JChem platform to the MMS database, they can conduct a Markush structure search through the JChem interface. First, users must define the domain of the query: searching the entire database is the default domain, but users can also choose to conduct the search within specific lists of records. The user then selects to add a "detail field." Under the "detail field" menu, they select the "vmns" option, and from the "vmns" menu they select "Markush structure." Users can upload a Markush structure MarvinSketch. Users then define the search type (i.e. full structure or substructure), and they define other structure query options (stereochemistry, atom matching, tautomer, and vague bond). Finally, users can add additional search terms in text fields, connected by Boolean operators to the structure query, in order to further narrow the search.

Narrow the query by adding search terms for the text fields of the Markush record.

According the the Markush structures guide on the ChemAxon website, "the following query features are supported in the query when searching Markush targets":[7]

  • Tetrahedral and double bond E/Z stereochemistry
  • Query atoms, including atom lists, not lists, generic query atoms (A, Q, M, etc.)
  • Query bond types, including any, single/aromatic, etc.
  • Tetrahedral and double bond E/Z stereochemistry
  • Atom query properties: a (aromatic), A (aliphatic), R (part of a ring), R0 (not part of a ring), D<n> (number of explicit connections)
  • Bond topology query properties (chain/ring)
  • Link nodes
  • Position variation bonds
  • Explicit H atoms in query only match explicit Hydrogens in the Markush target.

Simple R-group queries are supported when searching Markush targets:[7]

  • Does not have R-logic
  • Does not contain nested R-group definitions
  • An R-group is referenced only once
  • Number of enumerates does not exceed 100


Chemical Structure Drawing and Query Creation in JChem

Chemical structures in JChem can be drawn using MarvinSketch, the "integrated structure drawing tool of JChem."[8] The MarvinSketch user guide gives detailed instructions on how to utilize all features of MarvinSketch, including how to draw Markush structures and R-group queries with the software.

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

The MarvinSketch structure drawings can be uploaded directly to the query form, as illustrated below. Users choose to "Add detail field" and then select a "Markush structure" drawn in MarvinSketch to be added as a term in the query.

Create a query to search through the Markush structure database on Instant 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. According to the guide "Special search types: Markush structures" on the ChemAxon website, "all structural search types are allowed for Markush targets/tables. (DUPLICATE, SUBSTRUCTURE, SUPERSTRUCTURE, FULL and FULL_FRAGMENT search types.)"[7]

Select the type of Markush structure search for the query.

Finally, users can define other attributes of the structure query, such as:

  • Stereochemistry (On, Exact, Diastereomer, Enantiomer, or Off)
  • Double bond stereo check (All, Marked, or Off)
  • Atom matching (On, Exact, or Ignore for Charges, Isotopes, Radicals, and Valence)
  • Tautomer (On or Off)
  • Vague bond (Off, Ambiguous aromaticity 5-membered rings, Ring bonds "or aromatic", All bonds "or aromatic", or Ignore bond types)
The search options for the Markush structure allow you to broaden or narrow your query.

Once a user has selected the options to apply to the structure query and added any additional text field terms, they can run the query in the MMS database.


Viewing Bibliographic Records in JChem

Users can view the MMS bibliographic records on the ChemAxon JChem platform in either Grid view or Form view. These options are selected in the upper left menu, above the Query form. Users can either select "Grid view for Inventions," which displays the bibliographic data on the Markush patent document in a spreadsheet-like format, or users can select the Form view, which displays both text fields and an image of the Markush structure.

The Form view of the Markush patent record in Instant JChem.


Hit List and View Focus in JChem

In ChemAxon, 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.

Select to view the relevant R-groups for a Markush structure search result.

Relevant R-groups and parts of the scaffold will be highlighted (blue) in the focused view of the structure image.

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

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

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

Users can also choose to list all R-groups for both the selected Markush structure and the enumerations by selecting "Show R-Groups." These lists of R-groups are quite lengthy and therefore need to be selected and magnified in order to be readable.

The “Show R-groups” option generates a list of all R-groups in the Markush structure and enumerated structures.

Finally, in the menu of enumerated results according to a single Markush structure, users can select "Markush reduction according to the hit" in order to only view enumerations that match the original structure query. According to a Markush enumeration guide on the ChemAxon website, "This option is only active when you have run a substructure search on the Markush table and when you have a Markush Search license. In this mode the enumerated structures are limited to those that contain the substructure."[9]

Users can select “Markush reduction according to the hit” to only view enumerations that match the Markush structure.


Analyzing Results in JChem

Users can analyze the list of enumerations of a selected Markush structure in ChemAxon's JChem by selecting the "Filter" tab in the enumerated structure menu. According to the JChem help guide:[9]

This allows a Chemical Terms filter to be specified that is applied to each enumerated structure. Those enumerated structures that fail the filter are discarded. When a filter is set you may then see fewer structures than you set as the maximum as some may be discarded. To set a Chemical Terms filter double click on the panel and the editor opens. This is the same editor that is used when specifying a Chemical Terms filter for queries, and the filter specified must return a boolean value (true or false). This filter can be useful for filtering out non-drug-like structures or similar purposes. Note that it only applies to Full or Random enumeration as Markush reduction can generate partially enumerated structures for which properties cannot be calculated.
Filter the enumerations by user-defined chemical terms.

In the "Chemical terms filter" editor, users can select predefined chemical term filters listed under the “Favourites” drop-down menu.

Select popular chemical term expressions listed under “Favourites.”

Users can also manually enter their own chemical term expressions into the editor form. Suggested chemical terms will automatically appear as the user types.

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.

Users enter the desired chemical terms and select “OK” to filter the enumerations.


editors note iconEditor's Note:

The JChem features for Markush structure search and analysis which improve upon the available search and display features for MMS in STN Express and Questel Imagination include: Markush strucure enumeration, Markush hit reduction, and filtration of enumerated results based on chemical attributes.


ChemAxon Support Services

Users can access the Help menu through the main menu bar in JChem, which provides "access to user documentation, the license manager and general information about IJC and ChemAxon."[10]

The full user guides for Instant JChem Version 5.5 and MarvinSketch are available on the website. Users can access the Administrators guide for Instant JChem in order to learn how to install the system and link it to other databases.

Besides user guides, a free Technical Support Forum for ChemAxon product users is available.

Users can learn about the other support resources available through ChemAxon through this page on the company website. Contact information for sales, technical support, academic support, consultancy, and the head office is also available on the website.


ChemAxon Pricing

For JChem, users can find pricing information for Instant JChem, JChem for Excel, the Calculations Pack add-on, and the Instant JChem Enterprise Edition on the ChemAxon website under the "Webshop" section. Users can "buy up to 20 licenses in a single transaction," and a per-user license for the basic Instant JChem program is from $350.[11]


ChemAxon in Publishing and Content Curation and Delivery

ChemAxon works with publishers to provide delivery (particularly web based delivery) of chemical content and in production for curation. Selected relationships include Cengage, Elsevier, SureChem, Taylor and Francis, Thomson Reuters, and Wiley.


Sources

  1. 1.0 1.1 1.2 "JChem and Marvin 5.5. launched." ChemAxon website,http://www.chemaxon.com/news/jchem-and-marvin-5-5-launched/. Accessed July 30, 2011.
  2. "ChemAxon launches ‘live’ chemistry in Microsoft SharePoint." ChemAxon website, http://www.chemaxon.com/news/chemaxon-launches-%E2%80%98live%E2%80%99-chemistry-in-microsoft-sharepoint%E2%84%A2/. Accessed July 30, 2011.
  3. "Thomson Reuters and ChemAxon Partner to Help Speed Drug Discovery for Life Science Researchers." Thomson Reuters website, http://thomsonreuters.com/content/press_room/legal/376030. Published January 04, 2011. Accessed on January 06, 2011.
  4. 4.0 4.1 "Instant JChem." ChemAxon website, http://www.chemaxon.com/products/instant-jchem/. Accessed June 28, 2011.
  5. "Administration Guide of JChem - Version 5.5.01." ChemAxon website, http://www.chemaxon.com/jchem/doc/admin/. Accessed June 28, 2011.
  6. "Import and conversion of Markush DARC files." ChemAxon website, http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/vmn_files.html. Accessed June 28, 2011.
  7. 7.0 7.1 7.2 "Special search types: Markush structures." ChemAxon website, http://www.chemaxon.com/jchem/doc/user/query_markush.html. Accessed June 28, 2011.
  8. "JChem Query Guide." ChemAxon website, http://www.chemaxon.com/jchem/doc/user/queryindex.html. Accessed July 28, 2011.
  9. 9.0 9.1 "Markush Enumeration." ChemAxon website, http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/markush_enumeration.html. Accessed June 28, 2011.
  10. "Windows, Menus and Toolbars." ChemAxon website, http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/windows_menus_toolbars.html. Accessed June 30, 2011.
  11. "ChemAxon Software." ChemAxon website, http://www.chemaxon.com/shop/. Accessed July 1, 2011.

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