HECBioSim: The UK High End Computing Consortium for Biomolecular Simulation.

HECBioSim：英国生物分子模拟高端计算联盟。

• 批准号: EP/X035603/1
• 负责人: Syma Khalid
• 金额: $ 66.07万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FX035603%2F1
• 关键词: HECBioSim; UK; End; Computing; Consortium

Biomolecular simulations enable us to predict the behaviour of biological systems given the structures (or models) of the components. Combined with the structural biology and new advancements in machine learning methods, molecular simulations provide the scope for unprecedented insights into biomolecular systems. The level of detail afforded by these methods, along with their ability to rationalise and augment experimental data and their predictive power in generating new hypotheses are already enabling them to make significant contributions in a wide variety of areas that are crucial for healthcare, the environment, quality of life and consequently, to the economy. The UK biomolecular simulation community has a strong international reputation, with world-leading research in in drug design and development, biocatalysis, bionano-technology, chemical biology and medicine. This has recently been demonstrated by the enormous impact our work has made on research into the SARS-CoV2 virus, in helping identify target sites for vaccine and antiviral development and has lead to our members winning and being shortlisted for international prizes, establishing new collaborations with industrial partners and being key participants in large international consortia.Furthermore, in addition to our work on Covid-19, we have delivered outstanding research with impact in bionanotechology, drug design, AMR as well as in developing novel models (e.g. fluctuating finite elements models), methodologies (e.g. conversion between fine-grained and coarse-grained resolutions) and enabling technologies (e.g.tools for efficient submission of calculations) for application across the full spectrum of biophysical and biochemical sciences. We are now at a time when we can take giant leaps in terms of the scope of our work. Having access to the largest, most modern computing facilities in the UK is essential for this. Renewal of the Consortium will enable us to continue allocating time ARCHER2 and Tier 2 resources for our cutting-edge biomolecular simulations.We will place a special emphasis on reaching out to experimentalists (indeed we already have a strong reputation for doing this) 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 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 Nanopore Technologies and Exscientia. Many of these academic-industry collaborations have been strengthened and in some cases, been established on the basis of work done through HECBioSim allocations. The Consortium will continue to welcome new members from across the whole community including ECRs. Indeed we have an excellent track record of ECRs from within our community going on to independent academic posts. 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 more efficient simulations by harnessing tools from the machine learning field an augmenting them with our own codes to make best use of the UK HEC landscape.In summary, HECBioSim will expand our portfolio of collaborative endeavours with experimental scientists and those working in industry to harness expertise from all domains to inform our own work and thus to maintain the UK as a world-leader in biomolecular simulation.

生物分子模拟使我们能够预测给定组件的结构（或模型）的生物系统行为。结合了机器学习方法的结构生物学和新的进步，分子模拟为生物分子系统的前所未有的见解提供了范围。这些方法提供的细节水平，以及它们合理化和增强实验数据的能力及其产生新假设的预测能力已经使他们能够在对医疗保健，环境，生活质量以及对经济的各种至关重要的领域中做出重大贡献。英国生物分子模拟社区在药物设计和开发，生物催化，比奥纳诺技术，化学生物学和医学方面的世界领先研究。 This has recently been demonstrated by the enormous impact our work has made on research into the SARS-CoV2 virus, in helping identify target sites for vaccine and antiviral development and has lead to our members winning and being shortlisted for international prizes, establishing new collaborations with industrial partners and being key participants in large international consortia.Furthermore, in addition to our work on Covid-19, we have delivered outstanding research with impact in Bionanotechology，药物设计，AMR以及开发新型模型（例如有限元模型波动），方法论（例如，细粒度和粗粒分辨率和粗粒分辨率之间的转换）和促成技术（例如，用于有效提高计算的工具），以跨生物物理和生物学和生物学杂志的应用进行计算）。现在，我们正处于我们的工作范围方面的巨大飞跃。可以使用英国最大，最现代的计算设施。财团的更新将使我们能够继续为我们的尖端生物分子模拟分配时间Archer2和2级资源。我们将特别强调与实验者联系，实际上我们已经在这样做的强烈声誉了（我们已经在这样做的强烈声誉），并且在行业中工作以促进跨性别者和实验性的科学家之间的相互作用，以促进跨性别的科学家，并促进了跨越的科学家，并促进了整体化的群组，并促进了整体化的互动。仿真是药物设计和开发的组成部分。制药行业需要该领域训练有素的科学家以及新方法的发展（例如，用于预测药物结合亲和力，配体选择性和代谢）。该财团的成员与行业合作有良好的记录，以提供训练有素的科学家和新方法。例如，由财团成员培训的博士生最近在UCB，联合利华，牛津纳米孔技术和Exscientia担任职位。这些学术行业的许多合作都得到了加强，在某些情况下是根据通过Hecbiosim分配完成的工作建立的。该财团将继续欢迎包括ECRS在内的整个社区的新成员。的确，我们从社区内部到独立学术帖子的ECR有出色的记录。我们将继续使用HEC资源的生物分子模拟为专家和非专家开发计算工具和培训。我们建议开发新工具，通过利用机器学习领域的工具来增强我们的守则，以充分利用我们的英国景观。总而言之，Hecbiosim将扩大我们与实验性科学家的协作努力的组合，并在各行业中努力与所有领域合作，从而使所有领域的范围都保持良好的态度，从而将领域的忠实范围保持在公共方面，从而将领域与我们的工作保持一致。

项目成果

The liquid-to-solid transition of FUS is promoted by the condensate surface.

FUS 的液-固转变是由冷凝表面促进的。

• DOI: 10.1073/pnas.2301366120
• 发表时间: 2023
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Shen,Yi;Chen,Anqi;Wang,Wenyun;Shen,Yinan;Ruggeri,FrancescoSimone;Aime,Stefano;Wang,Zizhao;Qamar,Seema;Espinosa,JorgeR;Garaizar,Adiran;StGeorge-Hyslop,Peter;Collepardo-Guevara,Rosana;Weitz,DavidA;Vigolo,Daniele;Knowles,Tuom
• 通讯作者: Knowles,Tuom

Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates.

• DOI: 10.1002/advs.202207742
• 发表时间: 2023-09
• 期刊: ADVANCED SCIENCE
• 影响因子: 15.1
• 作者: Blazquez, Samuel;Sanchez-Burgos, Ignacio;Ramirez, Jorge;Higginbotham, Tim;Conde, Maria M.;Collepardo-Guevara, Rosana;Tejedor, Andres R.;Espinosa, Jorge R.
• 通讯作者: Espinosa, Jorge R.