Sachem: a chemical cartridge for high-performance substructure search

Abstract

BackgroundStructure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to the verification procedure. In substructure search, fingerprints are designed to capture important structural aspects of the molecule to aid the decision about whether the molecule contains a given substructure. Currently available cartridges typically provide acceptable search performance for processing user queries, but do not scale satisfactorily with dataset size.ResultsWe present Sachem, a new open-source chemical cartridge that implements two substructure search methods: The first is a performance-oriented reimplementation of substructure indexing based on the OrChem fingerprint, and the second is a novel method that employs newly designed fingerprints stored in inverted indices. We assessed the performance of both methods on small, medium, and large datasets containing 1, 10, and 94 million compounds, respectively. Comparison of Sachem with other freely available cartridges revealed improvements in overall performance, scaling potential and screen-out efficiency.ConclusionsThe Sachem cartridge allows efficient substructure searches in databases of all sizes. The sublinear performance scaling of the second method and the ability to efficiently query large amounts of pre-extracted information may together open the door to new applications for substructure searches.

Interoperable chemical structure search service

“…Overall, the service implementation can be viewed as an interoperable wrap of the structure search interface of the Sachem cartridge [11].…”

CyBy2: a strongly typed, purely functional framework for chemical data management

“…Groups with larger datasets might consider a hybrid approach: As chemical structures together with their fingerprints required in substructure and similarity searches typically make up the bulk of a chemical database, this information can still be stored in a relational database and these kinds of queries run using a chemical database cartridge such as RDKit [3] or Sachem [36], while additional structured data is still stored as a data tree. (A database cartridge is a way to enhance an existing database implementation with business logic from other domains.…”

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

“…Under each taxon name, clicking on the reference link will then display the scientific publication documenting the occurrence. (Kratochvíl et al, 2018). The engine is used by the Integrated Database of Small Molecules (IDSM) that operates, among other things, several dedicated endpoints allowing structural search in selected small-molecule datasets via SPARQL (Kratochvíl et al, 2019).…”