Molecular search techniques are invaluable tools in all cheminformatics systems including rational drug design, compound registration systems and laboratory information management systems. Often they provide a basis for more complex applications like functional group identification, bond cleavage, virtual reaction processing, standardization, toxic fragment identification, etc.

JChem, one of ChemAxon’s major suites of programs, provides a very rich set of features related to structural search which is described in this presentation from different points of view: interfaces and options, database solutions, formats and platforms, the performance of the JChem Base. The Oracle was extended to support chemical database operations through JChem Cartridge for Oracle which has got two examples in this presentation: SQL examples and SQL examples using Chemical Terms. The JChem tools can handle a wide variety of query features that are detailed below:

  • Atom query features
  • Query of SMARTS atoms
  • Bond and fragment query features
  • E/Z double bond stereo searching
  • Tetrahedral Chirality
  • Reaction search
  • R-group search
  • Explicit and implicit hydrogens
  • Canonicalization

ChemAxon’s JChem suite contains a broad range of chemical search facilities with a rich set of features besides the above mentioned ones. The final part of the presentation gives a proper overview about the Chemical Terms language, the Similarity search, the Maximum Common Subgraph and R-group decomposition. All the tools mentioned in this presentation are 2005 releases and built 100% on Java platform.

9th Annual InfoTechPharma® Conference, 15-16 March, 2005.