DC 13: Virtual screening and design of riboswitch ligands

PhD project description:

The PhD project will focus on using computational methods for hit discovery for the SAM-III, SAM-I/IV and FMN riboswitches. In particular, you will carry out structure-based virtual screening of ultra-large chemical libraries and chemical spaces containing millions to billions of compounds. Further, you will optimize the hits discovered by virtual screening and fragment screening (WP2) by designing analogues. The compounds will be either purchased or synthesised and tested for binding by fellow students.

Further, our collaborator Nicholas Pearce has developed software that allows analysing data resulting from crystallographic fragment screening (PanDDA). In collaboration with him, you will expand the PanDDA capabilities, so that also RNA crystals can be processed. You will subsequently apply this tool to analyse the crystallographic fragment screening data obtained in the TargetRNA network.