Chemical Informatics I: Conversion and Scanning of Chemical Images

Updated: 10 October 2003

I. Coversion of Chemical Images

A. Conversion of 2D Structural Data into 3D Format
1. STN Express with Discover!
• CONCORD (Tripos)
  • developed to convert 2D to 3D entries containing connection tables
  • uses a detailed table of bond lengths
  • also: atomic number, hybridization and bond type
2. CORINA
http://www2.chemie.uni-erlangen.de/software/corina/free_struct.html
• Works similarly to CONCORD
• uses a different approach to connect the ring systems:
  rings are fused and the energies of possible ring conformations are calculated using a crude force field.
B. SMILES to gif

• GIF/PNG-Creator for 2D Plots of Chemical Structures http://www2.ccc.uni-erlangen.de/services/gif.html
C. BABEL and Open Babel
• interconverts a number of file formats
• available for Unix, DOS, Mac
• FTP site: ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/

II. Programs to Search for Chemical Structures/Reactions in Documents

A. Accelrys's ChemExplorer
• recognizes ISIS/Draw Sketchfiles or ChemDraw files, Molfiles, Rxnfiles, SD and RD files, HTML pages, Word documents, Excel spreadsheets, etc.
• looks and works like the Windows Finder
• See the demo on the Accord ChemExplorer page
B. CLiDE: Chemical Literature Data Extraction
• SimBioSys produces CLiDE
• recognizes structures, reactions, and text from scanned images
• stores the information in ChemDraw or MOL file format
• See the demo screens on the CLiDE page

• Dymond (Dynamic Metadata on Demand)
  • Clicking on a structure or reaction in a primary journal initiates a database search
  • Integrates journal articles with information in databases or visualization software:
    • Beilstein, Combined Chemical Dictionary, Autonom
    • Chime representation
  • Future: property and spectra predictions and links to other databases/applications with structure searching http://www.chemweb.com/dymond
  • For a sample article, see the e-journal version of Tetrahedron Letters 2000, 41(15), 2511-2514.
    Screen shot of article page with Dymond links
    The Dymond window
    Seamless link to Beilstein record

• Produced by ChemAxon: http://www.chemaxon.com/marvin/
• handles molecules in various file formats including MDL mol, Compressed mol, unique SMILES, SMARTS, Sybyl mol, PDB, CML, XYZ, POV-Ray.