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/R029407/1
• 负责人: Syma Khalid
• 金额: $ 40.96万
• 依托单位: University of Southampton
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FR029407%2F1
• 关键词: UK; End; Computing; Consortium; Biomolecular

There is tremendous future scope for biomolecular simulation to provide unprecedented insights into biomolecular systems. The level of detail afforded by these methods, along with their ability to rationalise experimental data and their predictive power are already enabling them to make significant contributions in a wide variety of areas that are crucial for healthcare, quality of life and the environment. The UK biomolecular simulation community has a strong international reputation, with world-leading efforts in in drug design and development, biocatalysis, bionano-technology, chemical biology and medicine. HECBioSim has already delivered outstanding research with impact in bionanotechology, drug design and AMR. But we have only just scratched the surface and there is currently huge room for expansion. Having access to the largest, most modern computing facilities is essential for this. Renewal of the Consortium will enable us to continue allocating time ARCHER for cutting-edge biomolecular simulations.We will place a special emphasis on reaching out to experimentalists and scientists working in industry in order to foster interactions between computational and experimental scientists, and academia and industry to encourage integrated multidisciplinary studies of key problems.Biomolecular simulation and modelling is an integral part of drug design and development. The pharmaceutical industry needs well-trained scientists in this area, as well as the development of new methods (e.g. for prediction of drug binding affinities, ligand selectivity and metabolism). Members of the consortium have a strong track record of collaboration with industry to deliver trained scientists and new methodologies. For example, PhD students trained by consortium members have recently taken up positions in UCB, Unilever, Oxford Nanoimaging and even Sky Broadcasting as software developer. Many of these academic-industry collaborations have been strengthened by work done through HECBioSim allocations. The Consortium will continue to welcome new members from across the whole community. We will continue to develop computational tools and training for both experts and non-experts using biomolecular simulation on HEC resources. We propose to develop new tools that will enable inter-conversion between biomolecular systems at different levels of resolution thereby allowing users to tackle more ambitious 'grand challenges' than are currently feasible.In summary HECBioSim will foster collaborations between computational and experimental scientists between scientists working in industry and academia in all disciplines within biomolecular simulation to maintain the UK as a world-leader in this field.

生物分子模拟具有巨大的未来空间，可以为生物分子系统提供前所未有的见解。这些方法提供的详细程度，以及它们合理化实验数据的能力和预测能力，已经使它们能够在对医疗保健、生活质量和环境至关重要的各种领域做出重大贡献。英国生物分子模拟界享有很高的国际声誉，在药物设计和开发、生物催化、生物纳米技术、化学生物学和医学方面拥有世界领先的成果。 HECBioSim 已经在生物纳米技术、药物设计和 AMR 领域做出了具有影响力的杰出研究。但我们才刚刚触及表面，目前还有巨大的扩展空间。为此，拥有最大、最现代化的计算设施至关重要。联盟的更新将使我们能够继续为尖端生物分子模拟分配时间 ARCHER。我们将特别重视与工业界工作的实验学家和科学家的接触，以促进计算和实验科学家以及学术界和工业界之间的互动鼓励关键问题的综合多学科研究。生物分子模拟和建模是药物设计和开发的一个组成部分。制药行业需要该领域训练有素的科学家，以及新方法的开发（例如预测药物结合亲和力、配体选择性和代谢）。该联盟成员在与业界合作提供训练有素的科学家和新方法方面有着良好的记录。例如，由联盟成员培养的博士生最近在 UCB、联合利华、牛津纳米成像甚至天空广播公司担任软件开发人员。通过 HECBioSim 拨款完成的工作，许多学术与工业合作得到了加强。联盟将继续欢迎来自整个社区的新成员。我们将继续使用 HEC 资源上的生物分子模拟来开发计算工具并为专家和非专家提供培训。我们建议开发新工具，使不同分辨率水平的生物分子系统之间能够进行相互转换，从而使用户能够应对比目前可行的更雄心勃勃的“重大挑战”。总之，HECBioSim 将促进计算科学家和实验科学家之间的合作在生物分子模拟所有学科的工业界和学术界，保持英国在该领域的世界领先地位。

项目成果

Evaluating the use of absolute binding free energy in the fragment optimization process.

评估片段优化过程中绝对结合自由能的使用。

• DOI: http://dx.10.26434/chemrxiv-2022-cw2kq-v2
• 发表时间: 2022
• 作者: Alibay I

Membrane Interactions of a-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

多尺度分子动力学模拟、马尔可夫态模型和 NMR 揭示了 a-突触核蛋白的膜相互作用

• DOI: http://dx.10.1101/2020.06.18.156216
• 发表时间: 2020
• 作者: Amos S

Sharing Data from Molecular Simulations

共享分子模拟数据

• DOI: http://dx.10.26434/chemrxiv.9775493.v1
• 发表时间: 2019
• 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

Membrane Interactions of a-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR.

通过多尺度分子动力学模拟、马尔可夫状态模型和核磁共振揭示α-突触核蛋白的膜相互作用。

• DOI: http://dx.10.1021/acs.jpcb.1c01281
• 发表时间: 2021
• 期刊: The journal of physical chemistry. B
• 作者: Amos STA