The UK High-End Computing Consortium for Biomolecular Simulation

英国生物分子模拟高端计算联盟

基本信息

批准号：
EP/L000253/1
负责人：
Adrian Mulholland
金额：
$ 36.76万
依托单位：
University of Bristol
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2013
资助国家：
英国
起止时间：
2013 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FL000253%2F1
关键词：
UK End Computing Consortium Biomolecular

项目摘要

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.

使用强大的计算机的模拟可以显示生物分子如何在原子细节中“工作”。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的生长区域，对生物学做出了越来越重要的贡献。这是国际重要性越来越大的领域。生物分子的模拟补体实验在建立生物学的分子水平理解中：它们可以检验假设，并以原子水平的相互作用来解释和分析实验数据。已经开发了多种模拟技术，适用于生物分子科学中的一系列不同问题。生物分子模拟已经显示出其价值，可以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。它们有助于药物和催化剂的设计，并理解疾病的分子基础。模拟在开发生物分子科学核心的概念框架中发挥了关键作用，也就是说，理解生物分子移动和弯曲的方式 - 它们的动力学 - 它们的功能至关重要。从化学物理学和计算科学开发的方法将在包括药物开发和生物技术在内的生物分子科学方面开放令人兴奋的新机会。许多生物分子模拟要求高端计算（HEC）资源：例如大规模的生物机器模拟，例如核糖体，质子泵和电动机，膜受体复合物，甚至整个病毒。一个特殊的挑战是跨长度和时间表的仿真集成：不同类型的问题需要不同类型的模拟方法）。分子模拟越来越多地促成诸如生物技术，药物设计，生物催化和生物医学等领域。英国在CCP-BIOSIM（CCPBIOSIM.AC.UK）的EPSRC（2011年）的认可，英国在这一领域中拥有强大的社区，这是英国生物分子模拟合作计算项目在Life Sciences界面上的合作计算项目（以及随后奖励2012年加强参与资金的奖励）。我们认为，该领域对高端计算有一个明确，不断增长且可证明的需求，并提出了一个新的HEC联盟，用于生物分子模拟中。该财团与CCP-Biosim合作，将有助于将HEC带到更广泛的社区，包括非传统的用户和实验生物科学家，并吸引物理和计算机科学家参与生物学应用。