In my last post I described the basic details of how the fragment network is composed and how it allows queries for similar molecules that are “chemically intuitive”. Here I show how queries can be executed through the REST API and how this has turned out to be extremely useful in the virtual screening work we are doing on the SARS-Cov-2 main protease in collaboration with the Diamond Light Source.

In my last post I described how the fragment network can be used as a key part of a virtual screening project by providing allowing your initial hits to be expanded out to a large number of candidates to screen. In this post we describe how the fragment network works and why is more ‘chemically intuitive’ that traditional fingerprint based similarity search.

We’ve previously mentioned the fragment network and our Fragnet Search application that provides a user friendly way to search and explore the data in the fragment network. But we’ve not really explained the basis of the fragment network and how it can be utilised in a drug discovery program. This is the first is a series of posts that covers this topic.

We’ve been very busy recently helping out on the fragment screening program at the Diamond Light Source. They generated fragment hits of the SARS-Cov-2 main protease back in early March. See here for details.

With that data we’ve been running virtual screening using compounds expanded out from the fragment screening hits using the API of Fragnet Search. Details of the initial virtual screening workflow that was executed on usegalaxy.eu are described here and I, along with Simon Bray from the Freiburg Galaxy team, will be presenting this in session 3 of the Galaxy-ELIXIR webinar series on COVID-19 on 14 May 2020, 17pm CEST. Come along and hear the details. You will need to register first.

We’ll be describing various aspects of the work in more details in this blog at a later stage.

We’ve recently demonstrated our Fragnet Search application in a SaferWorldbyDesign webinar.

In it we demonstrate using the web application and programmatically accessing the REST API behind it.

Take a look at the recording on YouTube.

We’ve been working with the fragment network as part of our work with the fragment screening program at the Diamond Light Source for a couple of years now. The fragment network was conceived by Astex and provides a chemically intuitive way to identify similar compounds without the limitations of traditional fingerprint based similarity searching.