CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface
CCP-BioSim:生命科学界面的生物分子模拟
基本信息
- 批准号:EP/M022609/1
- 负责人:
- 金额:$ 30.03万
- 依托单位:
- 依托单位国家:英国
- 项目类别:Research Grant
- 财政年份:2015
- 资助国家:英国
- 起止时间:2015 至 无数据
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
"Everything that living things do can be understood in terms of the jigglings and wigglings of atoms" as Richard Feynman provocatively stated nearly fifty years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge. Experiments can provide detailed structures of biological macromolecules such as proteins, but it is hard to study directly how the structures of individual molecules change on short timescales as they function. Similarly it is not yet possible to study directly by experiment alone the molecular mechanisms of fast processes such as chemical reactions in enzymes or ion transport through membranes. Simulations based on fundamental physics offer the potential of filling-in these crucial 'gaps', modelling how proteins and other biomolecules move, fluctuate, interact, react and function.Physics-based simulations 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. Simulations have already shown their worth in helping to analyse how enzymes catalyse biochemical reactions, and how proteins adopt their functional structures. They can help in the design of drugs and catalysts, and in understanding the molecular basis of disease. And 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, demonstrating the truth of Feynman's assertion.Developing methods from chemical physics and computational science will open exciting new opportunities in biomolecular science, including in drug design and development, synthetic biology, biotechnology and biocatalysis. Much biomolecular simulation demands 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). We work to develop 'multiscale' modelling and simulation methods to tackle these large problems, in areas such as drug metabolism and transport.
正如理查德·费曼在近50年前挑衅性地指出的那样,“生物所做的一切都可以用原子的摆动来理解”。但是,我们如何才能“看到”这种摆动和摆动,并理解它是如何驱动生物学的呢?越来越多地,生物大分子的计算机模拟正在帮助迎接这一挑战。实验可以提供蛋白质等生物大分子的详细结构,但很难直接研究单个分子的结构在短时间尺度上如何随着它们的作用而变化。同样,仅靠实验还不可能直接研究快速过程的分子机制,如酶中的化学反应或离子通过膜的传输。基于基础物理的模拟提供了填补这些关键的“空白”的潜力,对蛋白质和其他生物分子如何移动、波动、相互作用、反应和功能进行建模。基于物理的模拟补充了实验,以建立对生物学的分子水平的理解:它们可以检验假设,并从原子水平上的相互作用来解释和分析实验数据。已经开发了各种各样的模拟技术,适用于生物分子科学中的一系列不同的问题。模拟已经证明了它们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方面的价值。它们可以帮助设计药物和催化剂,并有助于理解疾病的分子基础。模拟在发展目前处于生物分子科学核心的概念框架方面发挥了关键作用,也就是理解生物分子运动和弯曲的方式--它们的动力学--是它们功能的核心,证明了费曼断言的真实性。从化学物理和计算科学发展方法将在生物分子科学中开辟令人兴奋的新机会,包括药物设计和开发、合成生物学、生物技术和生物催化。许多生物分子模拟需要HEC资源:例如,对核糖体、质子泵和马达、膜受体复合体甚至整个病毒等生物机器的大规模模拟。一个特别的挑战是跨长度和时间尺度的模拟的集成:不同类型的问题需要不同类型的模拟方法)。我们致力于开发“多尺度”建模和模拟方法,以解决药物代谢和运输等领域的这些大问题。
项目成果
期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations.
从绝对结合自由能计算中的配体选择性预测。
- DOI:10.1021/jacs.6b11467
- 发表时间:2017-01-18
- 期刊:
- 影响因子:15
- 作者:Aldeghi M;Heifetz A;Bodkin MJ;Knapp S;Biggin PC
- 通讯作者:Biggin PC
Entropy of Simulated Liquids Using Multiscale Cell Correlation.
- DOI:10.3390/e21080750
- 发表时间:2019-07-31
- 期刊:
- 影响因子:0
- 作者:Ali HS;Higham J;Henchman RH
- 通讯作者:Henchman RH
Molecular dynamics simulation of the adsorption of mung bean defensin VrD1 to a phospholipid bilayer
- DOI:10.1016/j.foostr.2019.100117
- 发表时间:2019-07
- 期刊:
- 影响因子:0
- 作者:Huda A. Alghamdi;Lydia Campbell;S. Euston
- 通讯作者:Huda A. Alghamdi;Lydia Campbell;S. Euston
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Adrian Mulholland其他文献
QM/MM Study on Cleavage Mechanism Catalyzed by Zika Virus NS2B/NS3 Serine Protease
- DOI:
10.1016/j.bpj.2018.11.3005 - 发表时间:
2019-02-15 - 期刊:
- 影响因子:
- 作者:
Bodee Nutho;Adrian Mulholland;Thanyada Rungrotmongkol - 通讯作者:
Thanyada Rungrotmongkol
Adrian Mulholland的其他文献
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{{ truncateString('Adrian Mulholland', 18)}}的其他基金
Predictive multiscale free energy simulations of hybrid transition metal catalysts
混合过渡金属催化剂的预测多尺度自由能模拟
- 批准号:
EP/W013738/1 - 财政年份:2022
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
BEORHN: Bacterial Enzymatic Oxidation of Reactive Hydroxylamine in Nitrification via Combined Structural Biology and Molecular Simulation
BEORHN:通过结合结构生物学和分子模拟进行硝化反应中活性羟胺的细菌酶氧化
- 批准号:
BB/V016768/1 - 财政年份:2022
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
Commercialisation of VR for biomolecular design
用于生物分子设计的 VR 商业化
- 批准号:
BB/T017066/1 - 财政年份:2020
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
Predicting drug-target binding kinetics through multiscale simulations
通过多尺度模拟预测药物靶标结合动力学
- 批准号:
EP/M015378/1 - 财政年份:2015
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
BristolBridge: Bridging the Gaps between the Engineering and Physical Sciences and Antimicrobial Resistance
BristolBridge:弥合工程和物理科学与抗菌素耐药性之间的差距
- 批准号:
EP/M027546/1 - 财政年份:2015
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
Computational tools for enzyme engineering: bridging the gap between enzymologists and expert simulation
酶工程计算工具:弥合酶学家和专家模拟之间的差距
- 批准号:
BB/L018756/1 - 财政年份:2014
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
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 - 财政年份:2013
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
Inquire: Software for real-time analysis of binding
查询:实时分析结合的软件
- 批准号:
BB/K016601/1 - 财政年份:2013
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
CCP-BioSim: Biomolecular simulation at the life sciences interface
CCP-BioSim:生命科学界面的生物分子模拟
- 批准号:
EP/J010588/1 - 财政年份:2011
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
Adaptive Multi-Resolution Massively-Multicore Hybrid Dynamics
自适应多分辨率大规模多核混合动力学
- 批准号:
EP/I030395/1 - 财政年份:2011
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant
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CCP-BioSim:生命科学界面的生物分子模拟
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CCP-BioSim: Biomolecular simulation at the life sciences interface
CCP-BioSim:生命科学界面的生物分子模拟
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- 资助金额:
$ 30.03万 - 项目类别:
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CCP-BioSim: Biomolecular simulation at the life sciences interface
CCP-BioSim:生命科学界面的生物分子模拟
- 批准号:
EP/J010588/1 - 财政年份:2011
- 资助金额:
$ 30.03万 - 项目类别:
Research Grant