Accelerating rational drug design with multi-threaded array processors

Pharmaceutical exports contribute over 12 billion to the UK economy each year (UK Trade and Investment figures for 2004). However, this success is threatened by the decline in the number of successful new drugs developed each year (The American Food and Drug Agency approved 230 drugs in 1997 and only 28 last year). This sharp decline indicates the need for new ways to develop pharmaceuticals. Computational chemistry has the potential to deliver the necessary step-change. Currently used methods for computing binding affinities of drug molecules to protein hosts are efficient but lack reliability because they fail to capture the essential physics. Quantum mechanics provides a physically accurate representation of the interactions, but these calculations are currently too computationally expensive for commercial use. We will use our existing expertise to implement quantum mechanical methods parallelized over thousands of processor cores. This will be achieved firstly by parallelization over the 100-core processor architecture of ClearSpeed plc, and secondly over clusters of nodes containing this acceleration technology. The techniques that we will develop will be applicable to emergent multicore designs from companies such as Intel, and have the potential to make a major contribution to rational drug design.