The molecular search techniques represent an extremely wide range of solutions in all cheminformatics systems. This presentation starts with highlighting some crucial examples of applications: compound registration, database search, pharmacophoric group identification, functional group identification, cleavage bond identification, virtual reaction procession, standardization, toxical fragment identification.

JChem, one of ChemAxon’s major suites of programs, provides a very rich set of features divided into two major groups: one is atom by atom search (ABAS) or structural search, the other is similarity search. The following slides describe the structural search in the ChemAxon's JChem Base. The Oracle was extended to support chemical database operations through JChem Cartridge for Oracle which has got examples about using substructure and similarity searches and Chemical Terms examples. The JChem tools can handle a wide variety of query features that are detailed below:

  • Atomic features
  • Atomic SMARTS features
  • Bond and components features
  • Double bond stereo search
  • Tetrahedral chirality stereo search
  • Reaction search
  • R-group search
  • Hydrogens

Afterwards you can read about the functionalities that are related to the structural search: Standardizer, similarity search, R-group decomposition and pairs of molecules. Among these tools the Chemical Terms is emphasized in this presentation. The new Chemical Terms language is a beneficial complement to structural searches allowing data mining made easy.

Applications of Cheminformatics and Chemical Modelling to Drug Discovery, 8-19 November 2004