Breakthrough Molecular Dynamics Research via an Anton2 Supercomputer

通过 Anton2 超级计算机进行突破性分子动力学研究

• 批准号: 10615059
• 负责人: Philip D. Blood
• 金额: $ 38.53万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-12-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10615059
• 关键词: Academy; Area; Award; Awareness; Binding Proteins; Biological; Biology; Biomedical Research; Collaborations; Communities; Community Health Education; Creativeness; Data; Data Collection; Data Science; Data Set; Disease; Evaluation; FAIR principles; Funding; Gifts; Goals; Grant; Institution; Instruction; Ion Channel; Knowledge; Letters; Machine Learning; Membrane; Molecular; National Research Council; Process; Protocols documentation; Publications; Quality of life; Reporting; Research; Research Personnel; Research Project Grants; Research Support; Resources; Running; Science; Secure; Services; Supercomputing; System; Time; Training Programs; Underrepresented Populations; United States National Academy of Sciences; United States National Institutes of Health; Work; anxious; archive data; base; broadening participation research; computing resources; cost; data management; data mining; data sharing; improved; innovation; molecular dynamics; next generation; outreach; outreach program; price lists; protein folding; service providers; supercomputer; uptake; web portal

Project Summary In 2010, Pittsburgh Supercomputing Center (PSC) and D.E. Shaw Research (DESRES) partnered to make the Anton special-purpose molecular dynamics (MD) supercomputer available to the national biomedical research community for the first time. Anton enabled researchers to simulate biomolecular systems two orders of magnitude faster than any conventional supercomputer, allowing researchers access to critical multi- microsecond and longer timescales on which most biologically-significant molecular processes take place. In 2016, with operational support from NIH, DESRES made available a next generation Anton 2 system at PSC at no cost. This multimillion-dollar gift from DESRES, with NIH support, provided a unique opportunity for researchers to tackle even more groundbreaking biological questions by simulating systems as large as 700,000 atoms at a rate of multiple microseconds per day. The goal of this renewal project is to provide the national biomedical research community with continued access to this unique and powerful Anton 2 resource and to maximize the benefit of this resource to the community. Since 2010, PSC has supported 589 research projects conducted by 202 unique PIs on the Anton systems hosted at PSC. So far, these projects have resulted in 292 publications, many of which have had significant impact on their fields of research. These fields cover the entire spectrum of biomolecular processes that form the fundamental underpinnings of biology, including protein folding, ion channel selectivity and gating, membrane dynamics and organization, protein- ligand binding, and many others. Demand for Anton 2 is quite high, with 2-3x higher demand than can be met each year. Given this, our goals are focused not only on providing continued access but also on maximizing the value of this limited resource to the community—recognizing that the creativity of the broad, diverse Anton 2 research community is one of our most powerful resources for innovation. Anton 2 will be integrated as an XSEDE service provider, and the accessibility and impact of Anton 2 will significantly increase by engaging in their extensive broadening participation, outreach, and training programs. Through these outreach efforts, researchers at many more institutions will have the opportunity to use Anton 2, especially researchers from traditionally underrepresented groups in biomedical research. The hundreds of long-timescale MD trajectories researchers generate on Anton 2 constitute a unique and valuable dataset that can be used to gain additional biomedical knowledge and advance the application of machine learning protocols to augment molecular dynamics simulations. This important dataset will be available to researchers and educators worldwide through a web portal and co-located on the PSC's Bridges-2 system for classroom instruction and research, including reanalysis, machine learning, and data mining.

项目摘要 2010年，匹兹堡超级计算中心（PSC）和D.E. Shaw Research（DESRES）合作制作了 安东专用分子动力学（MD）超级计算机可用于国家生物医学研究 社区第一次。安东使研究人员能够模拟生物分子系统的两个订单， 比任何传统的超级计算机都快，使研究人员能够访问关键的多 微秒和更长的时间尺度上，大多数生物重要的分子过程发生。在 2016年，在NIH的运营支持下，DESRES在PSC提供了下一代Anton 2系统， 不花钱。在NIH的支持下，DESRES提供的这份价值数百万美元的礼物为以下方面提供了独特的机会： 研究人员通过模拟大到 以每天几微秒的速度移动70万个原子。这个更新项目的目标是提供 国家生物医学研究社区继续获得这一独特而强大的Anton 2资源 并尽量利用这些资源造福社会。自2010年以来，PSC已支持589项研究 由202个独特的PI在PSC托管的Anton系统上进行的项目。到目前为止，这些项目 发表了292篇论文，其中许多对他们的研究领域产生了重大影响。这些字段 涵盖了构成生物学基础的整个生物分子过程， 包括蛋白质折叠、离子通道选择性和门控、膜动力学和组织、蛋白质- 配体结合和许多其他的。对Anton 2的需求相当高，需求量是可满足需求量的2- 3倍 每年.鉴于此，我们的目标不仅集中在提供持续的访问， 这种有限的资源对社区的价值-认识到广泛的，多样化的安东的创造力 2研究社区是我们最强大的创新资源之一。安东2号将作为 XSEDE服务提供商，安东2的可访问性和影响力将通过参与 他们广泛的扩大参与，推广和培训计划。通过这些外联工作， 更多机构的研究人员将有机会使用Anton 2，特别是来自 传统上在生物医学研究中代表性不足的群体。数百个长时间尺度的MD轨迹 研究人员在安东2号上生成的数据构成了一个独特而有价值的数据集，可用于获得额外的 生物医学知识，并推进机器学习协议的应用，以增强分子生物学。 动力学仿真这一重要的数据集将通过以下方式提供给全世界的研究人员和教育工作者： 一个门户网站，并位于PSC的Bridges-2系统上，用于课堂教学和研究，包括 再分析、机器学习和数据挖掘。

项目成果

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.

• DOI: 10.1007/s00232-018-0026-y
• 发表时间: 2018-06
• 期刊: The Journal of membrane biology
• 作者: Gumbart JC;Ulmschneider MB;Hazel A;White SH;Ulmschneider JP
• 通讯作者: Ulmschneider JP

Modeling the molecular fingerprint of protein-lipid interactions of MLKL on complex bilayers.

• DOI: 10.3389/fchem.2022.1088058
• 发表时间: 2022
• 期刊: Frontiers in chemistry
• 影响因子: 5.5

Distinct Modes of Action of IAPP Oligomers on Membranes.

IAPP 低聚物对膜的独特作用模式。

• DOI: 10.1021/acs.jcim.1c00767
• 发表时间: 2021
• 期刊: Journal of chemical information and modeling
• 影响因子: 5.6
• 作者: Sepehri,Aliasghar;Nepal,Binod;Lazaridis,Themis
• 通讯作者: Lazaridis,Themis

Molecular Structure of the Long Periodicity Phase in the Stratum Corneum.

角质层长周期相的分子结构。

• DOI: 10.1021/jacs.9b08995
• 发表时间: 2019
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Wang,Eric;Klauda,JefferyB
• 通讯作者: Klauda,JefferyB

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).

• DOI: 10.1371/journal.pcbi.1006511
• 发表时间: 2018-10
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Chiang YC;Levsh O;Lam CK;Weng JK;Wang Y
• 通讯作者: Wang Y