Sachem GUI

Sachem is a high-performance chemical cartridge for fingerprint-guided substructure and similarity search. Sachem GUI allows quick access to this functionality on our Sachem installation. Indexed databases include up-to-date versions of PubChem and ChEMBL.

Search for compounds


We provide an indexing service that allows FAIR-style search in published chemical data. You can easily construct queries that contain chemical substructure and similarity search terms combined with protein or bioassay-related queries.

Search with SPARQL


PubChem RDF data exposed and searchable through an interoperable, semantic interface, using a custom high-performance SPARQL endpoint implementation. The service is still under development, but may already be used for processing many complicated queries.

ChemWebRDF app

Mission: Interoperability in small molecules

The main goal of IDSM is to aggregate many different sources of information about small molecules into a single, logically coherent and semantically interconnected information source. This is achieved using the semantic web technologies. The data is explored and queried by the SPARQL query language; allowing to search through the vast amount of published chemical RDF data.

IDSM technology

IDSM internals have been described in several articles:

  • Kratochvíl, M., Vondrášek, J., & Galgonek, J. (2018). Sachem: a chemical cartridge for high-performance substructure search. Journal of cheminformatics, 10(1), 27. doi:10.1186/s13321-018-0282-y
  • Kratochvíl, M., Vondrášek, J., & Galgonek, J. (2019). Interoperable chemical structure search service. Journal of cheminformatics, 11(1), 45. doi:10.1186/s13321-019-0367-2