This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
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This project focuses on multiscale simulations of disease-relevant proteins with intrinsically disordered regions (IDRs) and fully intrinsically disordered proteins (IDPs). Calculations include all-atom molecular dynamics simulations, enhanced sampling calculations, coarse-grain simulations, hotspot mapping, and cosolvent simulations to identify mechanisms and develop interventions targeting highly flexible and challenging proteins.
Python and PyTorch are used for custom analysis pipelines, and GROMACS 2024 with a range of force fields (Amber, CHARMM, MARTINI, custom) for MD simulations. eBDIMS coupled to GROMACS is used for sampling of large conformational changes. In-house workflows are executed at scale on HPC clusters using SLURM.