Publication of the week: Professor Paul Finn

Oliver Korb, Paul W. Finn & Gareth Jones, “The cloud and other new computational methods to improve molecular modelling”, Expert Opinion on Drug Discovery 2014, 9, 1121-1131.  doi: 10.1517/17460441.2014.941800.

Industrial, as well as academic, drug discovery efforts are usually supported by computational modelling techniques. Many of these techniques, such as virtual high-throughput docking, pharmacophore-based screening of conformer databases and molecular dynamics simulations, are computationally very demanding. Depending on the parallelisation strategy most applicable to the method, recent technologies based on central processing units (cloud and grid computing), or graphics processing units (GPUs), can be employed to accelerate their execution times considerably. This allows the molecular modeller to look at larger data sets, or to use more accurate methods.

The article introduces the recent developments in grid, cloud and GPU computing. The authors provide an overview of molecular modelling applications running on the above-mentioned hardware platforms and highlight caveats of the respective architectures, both from a theoretical and a practical point of view.

The architectures described can improve the molecular modelling process considerably, if the appropriate technologies are selected for the respective application. Despite these improvements, each of the individual computational platforms suffers from specific issues, which will need to be addressed in the future. Furthermore, current endeavours have focused on improving the performance of existing algorithms, rather than the development of new methods that explicitly harness these new technologies.

Read more on the Informa Healthcare website.

Professor Paul Finn is Professorial Research Fellow in the Clore Laboratory and Department of Applied Computing. He is also CEO of InhibOx, a spin-out company from the Chemistry Department of the University of Oxford focused on computer-aided drug design, and runs a drug design consultancy Affinity Drug Design.