Docking is often used in virtual screening to attempt to identify potential drug leads. To be effective you typically need to screen a large number of candidate molecules and that means you need to parallelise the process across multiple servers. This post describes how this can easily be done using AWS Parallel Cluster and Nextflow.
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.
One of our more interesting GitHub projects is the Docking Validation project. We use this to establish and document best practices in virtual screening tools (such as docking) and approaches to semi-automating and scaling these procedures.
We just completed a new ‘experiment’ that is related to our work at the Diamond Light Source’s XChem project which has done some amazing work on fragment based screening using XRay crystallography.