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/R029407/2
• 负责人: Syma Khalid
• 金额: $ 16.86万
• 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: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FR029407%2F2
• 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.

生物分子模拟在提供对生物分子系统的前所未有的洞察方面有着巨大的未来空间。这些方法所提供的细节水平，沿着它们合理化实验数据的能力和它们的预测能力，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。英国生物分子模拟社区具有很强的国际声誉，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具有世界领先的努力。HECBioSim已经在生物纳米技术、药物设计和AMR方面进行了出色的研究。但我们只是触及了表面，目前还有巨大的扩展空间。能够使用最大、最现代化的计算设施对此至关重要。联盟的更新将使我们能够继续分配时间ARCHER的尖端生物分子模拟。我们将特别强调接触实验学家和科学家在工业中工作，以促进计算和实验科学家之间的互动，生物分子模拟和建模是药物设计的一个组成部分，发展制药行业需要在这一领域训练有素的科学家，以及新方法的开发（例如，用于预测药物结合亲和力，配体选择性和代谢）。该联盟的成员在与工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，由联盟成员培训的博士生最近在UCB、联合利华、牛津纳米成像甚至天空广播担任软件开发人员。通过HECBioSim拨款所做的工作，许多学术界与工业界的合作得到了加强。该联盟将继续欢迎来自整个社区的新成员。我们将继续开发计算工具和培训专家和非专家使用HEC资源的生物分子模拟。我们建议开发新的工具，使生物分子系统之间的相互转换，在不同的分辨率水平，从而使用户能够解决更雄心勃勃的'大挑战'比目前可行的。总之，HECBioSim将促进计算和实验科学家之间的合作，在工业和学术界的科学家之间的工作在生物分子模拟的所有学科，以保持英国在这一领域的世界领先地位。

项目成果

Antibodies generated in vitro and in vivo elucidate design of a thermostable ADDomer COVID-19 nasal nanoparticle vaccine

• DOI: 10.1101/2023.03.17.533092
• 发表时间: 2023-03
• 期刊: bioRxiv
• 作者: Dora Buzas;H. Bunzel;Oskar Staufer;E. Milodowski;Grace Edmonds;beatriz Vidana Matteo;C. Schaffitzel;Sathish K. N. Yadav;K. Gupta;Charlotte Fletcher;M. Williamson;Alexandra Harrison;Ufuk Borucu;Julien Capin;Ore Francis;Georgia Balchin;Sophie Hall;Mirella Vivoli Vega;F. Durbesson;R. Vincentelli;Joe Roe;L. Wooldridge;R. Burt;Ross J L Anderson;A. Mulholland;J. Hare;Mick Bailey;A. Davidson;A. Finn;David Morgan;Jamie F S Mann;Joachim P. Spatz;F. Garzoni;J. Bufton;I. Berger

Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin.

• DOI: 10.1016/j.bpj.2022.11.2942
• 发表时间: 2023-01-03
• 期刊: BIOPHYSICAL JOURNAL
• 影响因子: 3.4
• 作者: Antonovic, Anna Katarina;Ochala, Julien;Fornili, Arianna
• 通讯作者: Fornili, Arianna

In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2

• DOI: 10.1093/abt/tbad024
• 发表时间: 2023-11-10
• 期刊: ANTIBODY THERAPEUTICS
• 作者: Buzas, Dora;Bunzel, Adrian H.;Berger, Imre
• 通讯作者: Berger, Imre

Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.

• DOI: 10.1021/acs.jctc.1c00547
• 发表时间: 2021-10-12
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Ansell TB;Curran L;Horrell MR;Pipatpolkai T;Letham SC;Song W;Siebold C;Stansfeld PJ;Sansom MSP;Corey RA
• 通讯作者: Corey RA

Photovoltaic enzymes by design and evolution

光伏酶的设计和进化

• DOI: 10.1101/2022.12.20.521207
• 发表时间: 2022
• 作者: Bunzel H