Background to Fragnet Search

Fragnet search is a set of tools inspired by the work done at Astex Pharmaceuticals and described in this publication doi:10.1021/acs.jmedchem.7b00809.

It describes methodology for creating a network of molecules based on their fragmentation and how Astex use this for selecting compounds for fragment based drug discovery. To understand how best to use Fragnet Search it is strongly recommended to read this paper.

The Astex paper describes the methodology very nicely, but the code was not released and being based on the Daylight toolkit is not a viable option today. The XChem project at the Diamond Light Source (Harwell, UK) saw the utility of the fragment network in their X-ray crystallograpy based fragment screening program, and Anthony Bradley (then at Diamond) re-implemented the fragment network methodology as a set of Python modules using the open source RDKit cheminformatics toolkit. This code can be found here. This is used in their Fragalysis application that forms the heart of their fragment screening follow up work.

We at Informatics Matters have been helping Diamond with this work for some time, and are now making sure these novel methodologies are available outside the context of fragment screening at Diamond. We believe it has a number of uses, but the prime ones are use for fragment screening and chemical building block selection. Fragnet Search is our current work in this area.