Macs in Chemistry

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An open source chemical structure curation pipeline using RDKit


I just thought I'd flag a recent paper in Journal of Cheminformatics described "An open source chemical structure curation pipeline using RDKit" DOI. As anyone who has had to curate a molecular dataset knows standardising the chemical structures is one of the absolutely key elements of the process.

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 component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures.

The ChEMBLStructurePipeline is freely available on GitHub

Or using Anaconda

conda install -c conda-forge chembl_sructure_pipeline
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