The UK High-End Computing Consortium for Biomolecular Simulation

英国生物分子模拟高端计算联盟

• 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

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.

使用功能强大的计算机进行模拟可以显示生物分子如何在原子细节上“工作”。例如，分子模拟可以显示药物与其生物靶标的结合、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且不断发展的领域，为生物学做出了越来越重要的贡献。这是一个日益重要的国际领域。生物分子的模拟补充了建立对生物学的分子水平理解的实验：它们可以测试假设并根据原子水平的相互作用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（例如蛋白质）方面的价值。细胞膜内。它们有助于药物和催化剂的设计，以及理解疾病的分子基础。模拟在发展生物分子科学核心概念框架方面发挥了关键作用，即理解生物分子移动和弯曲的方式（它们的动力学）对其功能至关重要。化学物理学和计算科学的开发方法将为生物分子科学（包括药物开发和生物技术）带来令人兴奋的新机遇。许多生物分子模拟需要高端计算 (HEC) 资源：例如生物机器的大规模模拟，如核糖体、质子泵和马达、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尺度的模拟集成：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) 的认可，这是英国生命科学接口生物分子模拟协作计算项目（以及随后的奖项） 2012 年“扩大参与”基金）。我们相信该领域对高端计算有着明确、不断增长和明显的需求，并在生物分子模拟领域提出了一个新的 HEC 联盟。该联盟与 CCP-BioSim 合作，将帮助将 HEC 推向更广泛的社区，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。

项目成果

Sharing Data from Molecular Simulations.

共享分子模拟数据。

• DOI: http://dx.10.1021/acs.jcim.9b00665
• 发表时间: 2019
• 期刊: Journal of chemical information and modeling
• 作者: Abraham M

Entropy of Simulated Liquids Using Multiscale Cell Correlation.

使用多尺度细胞相关性模拟液体的熵。

• DOI: http://dx.10.3390/e21080750
• 发表时间: 2019
• 期刊: Entropy (Basel, Switzerland)
• 作者: Ali HS

Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase.

色氨酸 7-卤素酶和色氨酸 5-卤素酶的分子动力学模拟的结构见解。

• DOI: http://dx.10.1021/acsomega.8b00385
• 发表时间: 2018
• 期刊: ACS omega
• 影响因子: 4.1
• 作者: Ainsley J

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo.

使用大正则蒙特卡罗对溴结构域结合袋中的水稳定性进行大规模分析。

• DOI: http://dx.10.1038/s42004-018-0019-x
• 发表时间: 2018
• 期刊: Communications chemistry
• 影响因子: 5.9
• 作者: Aldeghi M

Accurate calculation of the absolute free energy of binding for drug molecules.

准确计算药物分子结合的绝对自由能。

• DOI: http://dx.10.1039/c5sc02678d
• 发表时间: 2016
• 期刊: Chemical science
• 影响因子: 8.4
• 作者: Aldeghi M