CCPBioSim: Biomolecular Simulation at the Life Science Interface

CCPBioSim：生命科学界面的生物分子模拟

• 批准号: EP/T026308/1
• 负责人: Sarah Harris
• 金额: $ 44.05万
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FT026308%2F1
• 关键词: CCPBioSim; Biomolecular; Simulation; Life; Science

Biomolecular simulation aims to provide quantitative, predictive models for molecular structural biology from the level of enzyme catalysis up to cells. Modelling helps us to better understand the information we obtain from our experiments, and can provide insight in situations where experimental information is unavailable. Molecular simulations are based based on well-defined physics, and complement experiments: the unique insight they provide gives molecular level understanding of how biological macromolecules function. Simulations have proved crucial in analysing protein folding and self-assembly, mechanisms of biological catalysis, and the importance of dynamics in biomolecular function. Biomolecular simulations contribute to drug development (e.g. in structure-based drug design and predictions of metabolism) and design of biomimetic catalysts, and in understanding the molecular bases of disease and drug resistance. However, the complexity of biological molecules means that simulating them is extremely challenging, and remains an active areas of research internationally. CCPBioSim is the UK network of researchers that brings together expertise to support biomolecular simulators to perform the best calculations feasible within current scientific understanding and compute resources. We actively engage with the international community of biomolecular simulators, to ensure that the UK has access to the most up to date ideas and insights. We drive methodological developments to improve the state of the art and to integrate biomolecular simulation with emerging experimental tools. We embrace technological improvements that make our simulations faster, more accurate and accessible to a broader community of researchers. We engage with our community by organising conferences and training workshops, and we provide software that makes their simulations less challenging and more effective.

生物分子模拟旨在为从酶催化水平到细胞水平的分子结构生物学提供定量的预测模型。建模可以帮助我们更好地理解我们从实验中获得的信息，并且可以在无法获得实验信息的情况下提供见解。分子模拟基于定义良好的物理，并补充实验：它们提供的独特见解使生物大分子如何发挥作用的分子水平的理解。在分析蛋白质折叠和自组装、生物催化机制以及生物分子功能动力学的重要性方面，模拟已被证明是至关重要的。生物分子模拟有助于药物开发（例如基于结构的药物设计和代谢预测）和仿生催化剂的设计，以及了解疾病和耐药性的分子基础。然而，生物分子的复杂性意味着模拟它们是极具挑战性的，并且仍然是国际上研究的活跃领域。CCPBioSim是英国研究人员网络，汇集了专业知识，支持生物分子模拟器在当前科学理解和计算资源范围内执行最佳计算。我们积极参与生物分子模拟器的国际社会，以确保英国有机会获得最新的想法和见解。我们推动方法的发展，以提高艺术的状态，并将生物分子模拟与新兴的实验工具相结合。我们采用技术改进，使我们的模拟更快，更准确，并为更广泛的研究人员提供服务。我们通过组织会议和培训研讨会与社区互动，我们提供软件，使他们的模拟更容易，更有效。

项目成果

QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study.

MSOX 晶体学指导下的蛋白质晶体反应性的 QM/MM 模拟：亚硝酸铜还原酶案例研究。

• DOI: 10.1021/acs.jpcb.1c03661
• 发表时间: 2021
• 期刊: The journal of physical chemistry. B
• 作者: Sen K

Moving in the mesoscale: Understanding the mechanics of cytoskeletal molecular motors by combining mesoscale simulations with imaging

• DOI: 10.1002/wcms.1570
• 发表时间: 2021-08-21
• 期刊: WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
• 影响因子: 11.4
• 作者: Gravett, Molly S. C.;Cocking, Ryan C.;Harris, Sarah A.
• 通讯作者: Harris, Sarah A.