🎄12 Days of HPC 2022

Using ARC for virtual high-throughput ligand discovery: A journey through time 2009-2022​ ​

Blog post number 4 in our 12 days of HPC series from Faculty of Biological Sciences !

During the month of December we’re featuring blog posts from researchers from across the University of Leeds showcasing the fantastic work they do using our High Performance Computing system. Follow us @RC_at_Leeds to keep up to date with our 12 days of HPC blog series.

What’s your name?

Katie Simmons

What department do you work in?

Faculty of Biological Sciences

What research question are you trying to answer?

Can we identify new ways- either new proteins involved in diseases or new molecules to treat existing therapeutic target- to treat disease.

What tools or technologies do you use in your research? (Programming languages, packages, APIs)

I use software from OpenEye (ROCS, FRED, OMEGA), Schrodinger (Glide), Scripps Research Institute (AutoDock) and CCDC (GOLD).

How does HPC help your research?

HPC allows us to screen tens of millions of commercially available small molecules. If we used a single standard office PC we could only screen a few thousand at a time.

What is the potential impact of your research?

I can identify whether proteins implicated in disease can be targeted with a small molecule to affect their function in the body. This can lead to new drugs to treat diseases.

In your personal opinion what’s the coolest thing about your research?

One day, the molecules I select and test could become the basis for a new drug.

A small molecule (magenta) binding to a protein (green). The binding mode of this small molecule was predicted using docking studies carried out on the ARC cluster in Leeds and validated using X-ray crystallography.