An open source chemical structure curation pipeline using RDKit.

ABSTRACT:

Background

The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised.

Results

A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent compone

SUBMITTER: Bento AP 

PROVIDER: S-EPMC7458899 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature