Summary Systems with covalently bound ligands present a unique set of challenges in terms of modelling and compound design. Here, we examine a small set of ligands which bind to the MHC class I-related (MR1) protein of antigen-presenting cells (APCs) which, in turn, elicit an immune response modulated by Mucosal Associated Invariant T (MAIT) cells. We use a range of functionalities within the suite to dissect the various interactions made possible by the ligand binding and, in turn, consider how this information might be taken forward into further compound design allowing for both agonism and antagonism of the MAIT-MR1 interaction.
