University of Oxford leads cystic fibrosis research with Mac

Profiles in Success: University of Oxford

The University of Oxford is using bespoke Apple technology for groundbreaking research into cystic fibrosis, with researchers working towards a better understanding of both the causes and potential treatments for the disease. The research team is applying advanced biomolecular simulation techniques to a medically important fragment of the cystic fibrosis transmembrane conductance regulator (CFTR). The high performance Apple computing power they need is provided by the Apple Research & Technology Support programme (ARTS), which backs leading research across Europe.

“Apple is the perfect partner for biomolecular simulation, which is a great tool for understanding the basis of diseases and for developing drug treatments”, says Dr Ben Hall, Structural Bioinformatics & Computational Biochemistry Unit, University of Oxford. “We believe that Apple is the only company to offer the tight and seamless integration of web development, automation, high performance computing and UNIX tools on a single platform”.

The University of Oxford’s Structural Bioinformatics & Computational Biochemistry Unit is a pioneer in the study of membrane proteins such as CFTR. Membrane proteins are a major source of biological and medical information, accounting for about 25% of the genes encoded in the human genome and some 50% of known drug targets.

“Yet, although you can identify a lot of different membrane proteins, we don’t know the structures of very many of them”, says Dr Hall. “They are hard to study because they either sit across or on membranes. They are also much more fragile than many proteins that are soluble in water and can be studied in test tubes”.

Membrane protein research has been boosted in recent years by significant developments in biomolecular simulation. “Biomolecular simulation techniques have now advanced to the extent that it is possible to simulate the dynamics of relatively simple proteins for several microseconds”, says Dr Hall. “The results from these simulations compare favourably to experimental structures derived using Nuclear Magnetic Resonance spectroscopy”.

The drawback with simulations, however, is that their setup, monitoring and analysis is a manual process requiring many weeks work by researchers. This prohibits the systematic investigation of an individual protein by examining a large number of its mutants.

The solution for the Oxford research team seeking to study CFTR was to establish a simulation pipeline that will set up each model, perform extended simulations, analyse them and compare the results with others. For this, the team required dedicated high performance computing resources.

Although they might have found a partial solution to their computing requirements using their Department’s cluster of Linux systems, Dr Hall and his colleague Dr Philip Fowler were clear they needed dedicated high performance systems to deliver the project’s aims.

When the University called for project proposals in response to Apple’s ARTS programme, Dr Hall and Dr Fowler found an opportunity to build the research on their Apple platform of choice. They saw Apple technology would offer them a comprehensive technology solution.

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