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MarvinSketch is a chemical structure drawing tool designed by ChemAxon, a chemical software developer for the biotechnology and pharmaceutical industries. ChemAxon has been developing chemical software since 1998, and according to presentations from its User Group Meetings, has designed software for major pharma/biotech companies (such as AstraZeneca, GlaxoSmithKline, and Wyeth) as well as many search providers with an interest in chemical information (such as Wiley and Thomson Reuters).[1]

MarvinSketch in particular has been popular with free structure-searchable databases, such as SureChem and as a ready-to-go java applet that allows users to create advanced structure queries.

MarvinSketch can read a number of file formats for import, and will also interpret structures input via SMILES notation, peptide codes, IUPAC names, and more. The program can output structure files in a wide range of formats, but the patent search tools that rely on this program seem to require structure queries in .MOL file format. As of 2011, users can also "import Markush DARC files and save all features within Marvin’s default (mrv) format for sharing and subsequent editing."[2]

The product appears to support all the functionality needed to competently create a chemical structure query. In addition, ChemAxon is a particularly appropriate choice as a chemical structure drawing tool for a patent search system because its tools were designed with implicit understanding of Markush structure problems in patents.

The following is a list of notable features in the MarvinSketch application (some of which require plugins before they are supported):[3]

  • Support for multiple file types (MOL, MOL2, SDF, RX, RDF, SMILES, many more)
  • Copy/paste
  • Templates for commonly used molecular backbones and substitutions
  • 3D and 2D geometry editing and generation
  • Advanced query features, including generic atoms and bonds, allowed atom lists and "not lists" (groups of elements to exclude), and many more
  • Creating and editing molecule sets (without a database)
  • Structure annotation
  • Structure based calculations
  • Error checking (valence and reaction error checking)
  • Support for isotopes, charges, radicals, lone pairs and aliases
  • Markush enumeration

For a full list of features, see the detailed help guide. Also, see ChemAxon's Release News for more information with regards to new features.

MarvinSketch is advertised to developers on the basis that it can be easily customized. In fact, the program can be customized to look like two other common structure drawing programs, ISIS/Draw or Chemdraw.[4]

Another benefit to choosing ChemAxon as a provider of chemical structure drawing software is the company's small size and noted flexibility. Despite its small size, the company is able to maintain a 24 hour support function. [4]

Related Products

ChemAxon produces the Marvin family of products, which includes not only the MarvinSketch application for drawing and editing chemical structures, but also MarvinView, a product for viewing structure queries and reactions, and MarvinSpace, an application which creates publication-quality 3D images of macromolecules, as well as Marvin JS, which is a novel light-weight chemical editor suitable for generating standard chemical structures and simple queries on modern web browser pages without the need for installing Java. The newest member of the Marvin family is Marvin Live, a web based collaboration tool and meeting assistant to enable real time structure design for distributed research groups. ChemAxon's Plexus Suite is a web-based platform to access, display, search and analyze scientific data. A number of ChemAxon tools are integrated into the software suite providing a wide range of solutions from the registration process, through virtual library design and text mining to data analysis and database management. It is a versatile system suitable to the workflows of organizations ranging from small biotech start-ups to large pharmaceutical companies.

The company also produces the a series of IT Platform Toolkits: high performance, scalable toolkits for handling chemical content on your favourite database architecture, analysis and workflow platforms. IT Platform includes Biomolecule Toolkit, Compound Registration, JChem Cartridge, JChem Base, Standardizer, Structure Checker, JChem for Sharepoint.

Discovery Toolkit offers customizable functionality to generate, screen and analyze virtual chemical libraries while the company's Text Mining Suite provides reliable chemical name conversion and mining engine to and from nearly any biochemical, organic and inorganic structure. ChemAxon's Markush Search and Enumeration and Markush Editor enables Markush structures and patent/IP considerations in discovery and computational chemistry processes.

Wide range of ChemAxon technology is enabled in the largest workflow management systems and Spotfire’s analytical and visualization platform integration.

See more about the ChemAxon product portfolio here:

The latest release news of all ChemAxon products can be found here:


  1. ChemAxon User Group Meeting Archives, Accessed on January 23rd, 2015.
  2. "Advanced chemical drawing software." ChemAxon website, Accessed July 5, 2011.
  3. "Introduction to MarvinSketch." SureChem website, Accessed on September 17, 2008.
  4. 4.0 4.1 Dr. Wendy Warr, "Renaissance Meeting for ChemAxon." (Report on ChemAxon User Group Meeting, May 7-8, Visegrad, Hungary). MarvinSketch website, Accessed on October 10, 2008.

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