The UK High-End Computing Consortium for Biomolecular Simulation

使用功能强大的计算机进行模拟可以显示生物分子是如何在原子细节上“工作”的。例如，分子模拟可以显示药物与其生物靶标结合，酶如何催化反应，以及蛋白质如何折叠成其功能形式。生物分子模拟是一个充满活力和不断发展的领域，对生物学的贡献越来越大。这是一个日益重要的国际领域。对生物分子的模拟是对建立对生物学的分子水平理解的实验的补充：它们可以检验假设，并根据原子水平上的相互作用解释和分析实验数据。已经开发了各种各样的模拟技术，适用于生物分子科学中的一系列不同的问题。生物分子模拟已经显示出它们在帮助分析酶如何催化生化反应以及蛋白质如何采用其功能结构(例如在细胞膜内)方面的价值。它们有助于药物和催化剂的设计，并有助于理解疾病的分子基础。模拟在发展目前处于生物分子科学核心的概念框架方面发挥了关键作用，也就是理解生物分子运动和弯曲的方式--它们的动力学--是它们功能的核心。从化学物理和计算科学发展方法将在生物分子科学中开辟令人兴奋的新机会，包括在药物开发和生物技术方面。许多生物分子模拟需要高端计算(HEC)资源：例如，对核糖体、质子泵和发动机、膜受体复合体甚至整个病毒等生物机器的大规模模拟。一个特别的挑战是跨长度和时间尺度的模拟的集成：不同类型的问题需要不同类型的模拟方法)。生物分子模拟对生物技术、药物设计、生物催化和生物医学等领域的贡献越来越大。英国在这一领域拥有强大的社区，这一点得到了EPSRC最近(2011年)建立的CCP-Biosim(ccpBiosim.ac.uk)、英国生命科学界面生物分子模拟合作计算项目(以及随后在2012年授予的“扩大参与”基金)的认可。我们认为，在这一领域对高端计算的需求是明确的、不断增长的和明显的，并提出了一个新的HEC生物分子模拟联盟。该联盟将与CCP-Biosim合作，帮助将HEC带到更广泛的社区，包括非传统用户和实验生物科学家，并让物理和计算机科学家参与生物应用。

Simulations using powerful computers can show how biological molecules 'work' in atomic detail. For example, molecular simulations can show drugs bind to their biological targets, how enzymes catalyse reactions, and how proteins fold into their functional forms. Biomolecular simulation is a vibrant and growing area, making increasingly significant contributions to biology. It is an area of growing international importance. Simulations of biological molecules 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. Biomolecular 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 development and biotechnology. Much biomolecular simulation demands high end computing (HEC) 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).Biomolecular Simulations are contributing increasingly to areas such as biotechnology, drug design, biocatalysis and biomedicine. The UK has a strong community in this field, recognized by the recent (2011) establishment by EPSRC of CCP-BioSim (ccpbiosim.ac.uk), the UK Collaborative Computational Project for Biomolecular Simulation at the Life Sciences Interface (and the subsequent award of 'widening participation' funds in 2012). We believe there is a clear, growing and demonstrable need for high-end computing in this field, and propose a new HEC Consortium in biomolecular simulation. Working with CCP-BioSim, this Consortium will help bring HEC to a wider community, including non-traditional users and experimental bioscientists, and engage physical and computer scientists in biological applications.