Wednesday, February 19, 2014

RDKit Knime Workflows II: Reaction enumeration

Another workflow from the RDKit workshop at the Knime UGM in Zürich

This one deals with reaction-based library enumeration. It starts by reading in a set of compounds from the Zinc BB set, filters those by properties, and then uses the RDKit Functional Group Filter node to pick subsets that are compatible with the reaction. After some final randomization, the library is enumerated using an RDKit Two Component Reaction node to attach the building blocks to a core.

The results look like this:

Since the molecules share a common core, I've taken the additional step of generating 2D coordinates where those cores are aligned in order to make it easier to see how the products are related.

Until I figure out how to host these in a sensible way on a public knime server, I'll just provide things via dropbox links.
Here's the data directory that is used in this and all other workflows:
And here's the link to this workflow:

No comments: