CCP-BioSim: Biomolecular simulation at the life sciences interface

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Biomolecular simulation is a vibrant and growing area, making increasingly significant contributions to structural and systems biology. Physics-based simulations complement experiments in building a molecular level understanding of biology: they can test hypotheses and interpret and analyse experimental data in terms of interactions at the atomic level. A wide variety of simulation techniques have been developed, applicable to a range of different problems in biomolecular science. Simulations have already shown their worth in helping to analyse how enzymes catalyse biochemical reactions, and how proteins adopt their functional structures e.g. within cell membranes. They contribute to the design of drugs and catalysts, and in understanding the molecular basis of disease. Simulations have played a key role in developing the conceptual framework now at the heart of biomolecular science, that is, the understanding that the way that biological molecules move and flex - their dynamics - is central to their function. Developing methods from chemical physics and computational science will open exciting new opportunities in biomolecular science, including in drug design and development, biotechnology and biocatalysis. Much biomolecular simulation demands HPC resources: e.g. large-scale simulations of biological machines such as the ribosome, proton pumps and motors, membrane receptor complexes and even whole viruses. A particular challenge is the integration of simulations across length and timescales: different types of simulation method are required for different types of problems).We propose to establish a new collaborative computational project in biomolecular simulation at the life sciences interface, CCP-BioSim. CCP-BioSim will be an inclusive wide-ranging project, bringing together chemists, physicists and chemical engineers as well as researchers from all branches of 'molecule-oriented' biochemistry and biology. Our aim will be to involve experimentalists and computational specialists, sharing the belief that the best science can be done when theory and experiment are closely integrated. We will invite all current CCPB members (more than 300) to join CCP-BioSim, and also any other researchers who are interested. Members will be informed of activities via the CCP-BioSim mailing list and the CCP-BioSim website. CCP-BioSim will aim to identify methodological and computational challenges in the field, and to foster develoments to meet these scientific challenges. Involvement of early career academics will also be an important goal: the training workshops we will run will help in establishing research groups. CCP-BioSim will also provide a networking and collaboration framework. The strategy will be to concentrate on activities that promote and facilitate high-impact biomolecular research. We will foster close and innovative interactions between computational and experimental scientists, encouraging integrated multidisciplinary studies. CCP-BioSim will develop and provide training and tools to lower the barrier to non-experts becoming proficient and productive users of biomolecular simulation techniques. We will also work to develop and apply advanced methods. Engagement with experimentalists is crucial to ensure that the methodologies delivered are relevant to biological problems. This is a rapidly developing field: the best science comes from new simulation techniques and state-of-the-art (especially high performance computing (HPC)) hardware and software, requiring methodological development and significant and varied software development effort, in the context of UK and international projects.