Large Scale Protein Interactions – Application to Virus Assembly and Membrane Protein Association

Abstract

In this application we advance the state-of-the-art in molecular simulation using the Gromacs software on the DEISA-operated HPC infrastructure. Both software and hardware will be pushed towards new limits in this project where we are studying several important processes in the life cycle of a virus on atomic level. We will use a multi-scale approach, aimed at constructing accurate coarse-grained models from the simulation data which in a subsequent stage will allow the sizes of the studied systems to be increased further. The spatial and temporal scales covered in this computational project are clearly extreme according to today's standards but this work will inevitably open doors to a new era of biological computer modelling and simulation applications, with a direct potential to develop new anti-viral therapies. This work combines excellent scientific knowledge with truly high computational ambitions where versatile and highly optimized all-European simulation software will be used in a trans-European GRID structure of modern massively parallel supercomputers.