Speedy SMILES ChEMBL Preprocessing and Benchmarking

This workflow demonstrates the use of the Vernalis Speedy SMILES nodes to pre-process and filter a table of molecules from ChEMBL prior to subsequent processing in a chemical toolkit. The Vernalis benchmarking nodes are used to assess timing.

The processing is carried out within a component to enable streaming execution, which results in considerable timesavings. A Vernalis Benchmark Start/End loop surrounds the component to demonstrate the benchmarking functionality and also to allow the user to investigate the effect of using Streaming or non-streaming execution. The component contains the same nodes and annotations as those within the lower Benchmark loop which are not streamed

The top port of the component contains 'kept', desalted molecules, the bottom rejected molecules and the reason for rejection

The example contain 5000 compounds from ChEMBL21. The full set can be downloaded from the linked source (ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_21/chembl_21_chemreps.txt.gz). Please note that the downloaded file has to be unzipped prior to reading in with the file reader node.

External resources

• ChEMBL downloads