Computational Biomedicine – SuperMUC Allocation

A number of CompBioMed partners have been awarded a two year project at Leibniz Supercomputing Centre with an allocation on SuperMUC of 28 million core hours over two years, effective immediately. The project is led by Prof Dr Dieter Kranzmüller, Director of LRZ and Professor of Computer Science at Ludwig Maximillians Universitet, Munich. Partners include Prof Peter Coveney of the Centre for Computational Science at UCL, together with Dr Herman van Vlijmen of Janssen. The last two are core partners within CompBioMed, while LRZ is an Associate Partner.

Much of this award is concentrated on executing advanced workflows centred on molecular dynamics simulation of ligand-protein interactions, exploiting the development of important software services and tools by the UCL and LRZ teams. The central quantities of interest when assessing a potential drug are the thermodynamics (binding affinity or binding free energy) and kinetic (on- and off-rates) properties of its binding to the target protein. Historically, the pharmaceutical industry has avoided engagement with molecular dynamic and high performance computing due to the lack of accuracy and reproducibility, and long turnaround times. The purpose of current award is to develop high fidelity, computationally based, predictive mechanistic models of biomedical systems which can be applied in support of drug discovery and personalised medicine utilizing today’s top-level computational infrastructure. SuperMUC is a Tier-0 resource, meaning it is one of the international class of supercomputers, to designate that it supports projects which are internationally leading and command an equivalent scale of supercomputing.

One particular strength of the planned work is the collaboration between UCL, LRZ and Janssen R&D to study large, legacy internal datasets from Janssen. Our work in this area, in developing and applying the Binding Affinity Calculator (BAC) is helping to transform the field, making free energy calculations rapid, accurate, precise and reproducible. It requires access to powerful computational resources, of the kind available on SuperMUC.

The award coincides with the publication of a special report (available here) celebrating ten years of the Gauss Centre for Supercomputing, which features an article on Benefitting Public Health, based on UCL-CCS’s Giant Worflow performed across the combination of the entirety of Phases 1 and 2 of SuperMUC in June 2016. This was deemed to be one of the major accomplishments of the Gauss Center for Supercomputing in the ten year period of its existence. You can read the article on pages 6 & 7 in the following link.