Mapping Fitness and Free Energy Landscapes of Proteins

绘制蛋白质的健康度和自由能景观

• 批准号: 10577469
• 负责人: Ronald Levy
• 金额: $ 21.46万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10577469
• 关键词: 7 year old; Algorithmic Software; Biophysics; Computational Biology; Computer Systems; Computers; Computing Methodologies; Development; Equipment; Free Energy; Funding; High Performance Computing; Hybrids; Life Cycle Stages; Machine Learning; Problem Solving; Protein Dynamics; Proteins; Research; Research Personnel; Research Project Grants; Research Support; Resources; Scientist; Structure; System; United States National Institutes of Health; computational chemistry; computer cluster; computing resources; experience; fitness; high end computer; molecular dynamics; parent grant; structural biology

Abstract, Funds are requested to purchase computer equipment to support the research projects described in the parent grant NIH 1R35GM132090 “Mapping Fitness and Free Energy Landscapes of Proteins” (R.M. Levy, PI). The PI is a computational scientist with forty years of experience in computational structural biology and biophysics. The research described in the parent grant is focused on the development and application of computational methods for studying the structure, function, and dynamics of proteins. All of the projects supported by NIH 1R35GM132090 rely on access to state-of-the-art computational resources. Since 2015, advances in software and algorithms have led to a significantly greater focus on GPU implementations for machine learning and for solving problems in computational chemistry, biophysics, and structural biology. Access to the latest GPU hardware is essential for the successful completion of the research described in the parent grant. The PI requests a supplement to purchase 8 NVIDIA A100 40GB PCIe GPUs, with double the number of GPU cores and triple the bandwidth relative to the current consumer-level GPUs the PI currently has access to, and they are much better optimized for high-performance computing. The new GPUs will be connected to an existing shared computer cluster, the Center for Biophysics and Computational Biology Research Resource (CB2RR) cluster, which supports NIH funded researchers. The GPUs will be connected to the cluster using high- throughput, low overhead InfiniBand HDR 200 Gbps connections, which will be purchased with the GPUs. In addition, funds are requested to upgrade the storage system of the computer cluster with a 500TB RAID-6, as the current hard disks are now out of warranty and at the end of their life cycle. This system will excel at accelerating highly parallelized GPU-only and CPU-GPU hybrid molecular dynamics simulations and machine learning applications as described in NIH 1R35GM132090.

摘要， 要求提供资金，以购买计算机设备，以支持母项目中所述的研究项目 授予NIH 1R35GM132090“Mapping Fitness and Free Energy Landscapes of Proteins”（R.M. Levy，PI）。的PI 是一位计算科学家，在计算结构生物学和生物物理学方面拥有四十年的经验。 在父母补助金中描述的研究集中在计算的发展和应用上。 研究蛋白质结构、功能和动力学的方法。NIH支持的所有项目 1 R35 GM 132090依赖于对最先进的计算资源的访问。自2015年以来，软件的进步 和算法的发展，使得人们更加关注用于机器学习和 解决计算化学、生物物理学和结构生物学中的问题。访问最新的GPU 硬件对于成功完成母基金中所述的研究至关重要。的PI 请求追加购买8个NVIDIA A100 40 GB PCIe GPU，GPU核心数量加倍 并将带宽相对于PI当前可访问的当前消费级GPU增加三倍，而且他们 更好地优化了高性能计算。新的GPU将连接到现有的 生物物理与计算生物学研究资源中心（CB 2 RR） 集群，支持NIH资助的研究人员。GPU将使用高- 吞吐量、低开销的InfiniBand HDR 200 Gbps连接，将随GPU一起购买。在 此外，还要求提供资金，用500 TB RAID-6升级计算机集群的存储系统， 目前的硬盘已超出保修期，并处于其生命周期的末期。该系统将擅长于 加速高度并行化的纯GPU和CPU-GPU混合分子动力学模拟和机器 如NIH 1 R35 GM 132090中所述的学习应用程序。