Chemical cartridge optimized for high speed indexing and search performance

Dotmatics Pinpoint is a chemical cartridge for indexing and searching chemistry within Oracle databases.

What it does

Pinpoint enables indexing of chemical structures, calculations of physical chemical properties and substructure searches within an Oracle database. It is used to support structure searching with Dotmatics Browser, check for structural uniqueness and register molecules in Dotmatics Register, and store and search chemical reactions in Dotmatics Studies Notebook.


  • Performant – among the fastest index and search times of any commercially available cartridge
  • Chemically intelligent – exact, substructure and superstructure searching and property calculation
  • Simple – simple installation with no external services required
  • Integrated – fully integrated with Dotmatics Browser, Studies Notebook and Register
  • Collaborative – supports Oracle 12c, optimized for cloud installations to support applications used in external collaborations
  • Open – SQL interface for use by application developers

Key Features

  • Exact, superstructure and substructure search capability
  • Stereochemistry, aromaticity, tautomers and physiochemical property calculation
  • High performance search: sub-second substructure searches on multi-million compound databases
  • High performance indexing: Indexes more than four thousand structures per second on a single desktop CPU
  • Supports all versions of Oracle from XE to Enterprise
  • Support for Oracle 12c - designed for in-the-cloud deployment
  • Developed in collaboration with Astex Therapeutics
We deployed the whole Dotmatics Platform. Dotmatics Pinpoint is the chemical cartridge that underpins our chemistry registration, notebook and query system. We found that it has good performance standard for indexing and good query features. Definitively a good quality and robust cartridge.System Administrator, Biotech company, Norway