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Databases for Chemists and Chemical Engineers

MDL Databases Available at Stanford University

Databases Available

The following databases are provided by MDL Information Systems, Inc.:

Subject Type Name Description Documentation (note)
Bioactivity Molecule MDL-Drug Data Report-3D Description from MDL
National Cancer Institute Database-3D Description from MDL
Chemical Supplier Molecule Available Chemicals Directory (ACD)-3D Description from MDL
Metabolism Reaction Metabolite Description from MDL
Synthesis Reaction ChemInform Reaction Library Description from MDL
Comprehensive Heterocyclic Chemistry (CHC) n/a n/a
Organic Syntheses (ORGSYN) Description from MDL
Reference Library of Synthetic Methodology Description from MDL

(note) User manuals are also available on Reserve in Swain Library.

Desktop Software Needed

A suite of software programs are used to query and manipulate search results from the above files. See the instructions for downloading and configuring ISIS, Chime Pro and Central Library software (no account is needed to download this software).

Training sessions will be offered in the near future.

  • ISIS/Draw is a full featured chemical drawing package that produces publication quality graphics and also serves as a query drawing tool for searching ISIS. Macintosh and Windows versions available.
    More information: MDL’s ISIS/Draw page (
    Download (free for academic users, registration required): MDL’s Download page ( (Stanford only).
  • ISIS for Excel is an Excel add-in that provides the search, display, and manipulation capabilities of ISIS/Base for chemical structures and related data, entirely within Excel. Macintosh and Windows versions available.
    More information: MDL’s ISIS for Excel page (
  • Chime Pro, a Netscape or Internet Explorer plug-in, searches and displays chemical structures, reactions, 3D models and associated data from within your web browser. It renders “live” chemical structures that can be rotated, reformatted, and saved in files for use with other software programs.
    More information: MDL’s Chime Pro page (
    Download: Macintosh, PC (Stanford only).
  • Central Library is a ready-to-use, desktop software application designed to help researchers manage – at the product level – the chemical and biological data generated by combinatorial chemistry processes.
    More information: MDL’s Central Library page (

MDL Accounts for Searching

The MDL databases are available to students, faculty, visiting scholars, postdocs, and staff at Stanford University. Users may also perform searches in the Swain Chemistry and Chemical Engineering Library. Faculty may request a free MDL account from the Bioinformatics Resource Facility for their lab group.

The Swain Library account will support coursework that needs access to the MDL databases. Each account supports multiple simultaneous users. Accounts will also include disk space for storing locally created files. Please contact Grace Baysinger,, (650) 725-1039 for more information on the instruction and use of the MDL software and databases.

Copyright and Usage Limitations

All users need to read the important information in the MDL copyright and usage limitations page before using these databases.

Frequently Asked Questions & Help

The FAQ page contains hardware and software requirements as well as tips and support information for using the MDL databases.

Emily Wixson at the University of Wisconsin developed documentation for using MDL files ( While the way we connect is different, the instructions Emily assembled for searching the files is the same for both institutions.

Contact People:

  • MDL Accounts: Lee Kozar,, Bioinformatics Resource Facility, (650) 497-4483
  • Instruction & Use of Software/Databases: Grace Baysinger,, Swain Library of Chemistry and Chemical Engineering, (650) 725-1039

The MDL databases are being made available through the collaborative efforts of the Bioinformatics Resource Facility in the Medical School, the Swain Chemistry and Chemical Engineering Library, and Stanford’s Department of Environmental, Health and Safety.

Last modified: August 29, 2007

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