UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers

By Jon Chambers, M. Davies, Anna Gaulton, G. Papadatos, Anne Hersey, John P. Overington. 2014

30 citations recorded by the source corpus.

UniChem is a low-maintenance, fast and freely available compound identifier mapping service, recently made available on the Internet. Until now, the criterion of molecular equivalence within UniChem has been on the basis of complete identity between Standard InChIs. However, a limitation of this approach is that stereoisomers, isotopes and salts of otherwise identical molecules are not considered as related. Here, we describe how we have exploited the layered structural representation of the Standard InChI to create new functionality within UniChem that integrates these related molecular forms. The service, called `Connectivity Search' allows molecules to be first matched on the basis of complete identity between the connectivity layer of their corresponding Standard InChIs, and the remaining layers then compared to highlight stereochemical and isotopic differences. Parsing of Standard InChI sub-layers permits mixtures and salts to also be included in this integration process. Implementation of these enhancements required simple modifications to the schema, loader and web application, but none of which have changed the original UniChem functionality or services. The scope of queries may be varied using a variety of easily configurable options, and the output is annotated to assist the user to filter, sort and understand the difference between query and retrieved structures. A RESTful web service output may be easily processed programmatically to allow developers to present the data in whatever form they believe their users will require, or to define their own level of molecular equivalence for their resource, albeit within the constraint of identical connectivity.

Subfields: Computational Theory and Mathematics, Information Systems and Management, Molecular Biology

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Citations in the corpus

The ChEMBL database in 2017 (2016, background): “The ‘core’ of the resource continues to be molecule–target interaction data curated from the published literature, but as outlined above and in previous reviews (1,2,51,57,58) this has been expanded both in terms of data content, annotation and infrastructure.”
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands (2015, background): “UniChem and PubChem now exceed 90 and 60 million entries respectively, with nearly 14 million structures added in 2014 alone (2,3).”