RAPID: Folding@home and COVID-19

RAPID：Folding@home 和 COVID-19

• 批准号: 2032663
• 负责人: Gregory Bowman
• 金额: $ 20万
• 依托单位: Washington University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-15 至 2021-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2032663&HistoricalAwards=false
• 关键词: RAPID; Folding; home; COVID; 19

The SARS-CoV-2 virus uses numerous proteins to infect human cells, evade an immune response, and replicate itself. These proteins have moving parts that are essential to their function. Understanding the way the proteins move and change conformation will provide novel insights into viral biology and could potentially reveal new therapeutic opportunities. Researchers supported by this award are simulating the SARS-COV-2 proteins using the Folding@home distributed computer, which pools the computational resources of volunteer citizen scientists across the globe to run simulations on their personal computers. As a result of huge public interest and very productive interactions with major technology corporations, the Folding@home network now provides access to over 23 million CPU cores and 600,000 GPUs, making the network roughly 10-times more powerful than the world’s fastest traditional supercomputer. Support from this award will provide much needed upgrades to the cyberinfrastructure required to effectively harness this unprecedented computational resource and engage productively with the millions of people now participating in the effort to better understand SARS-COV-2. Results of the research effort will be published in peer-reviewed journals, presented at scientific meetings, and distributed broadly by social media and popular press.Folding@home is one of the largest and most successful distributed computing projects in the world. Current research efforts on the SARS-COV-2 include a dynamic analysis of every viral protein and free energy perturbation modeling of more than 50,000 small molecule interactions to identify possible starting points for therapeutics. Searching for cryptic binding sites is a major focus of the effort and early results are promising. With support from this award, improvements in the Folding@home TCP/IP stack, work collection servers, and back-end analysis servers will be conducted to increase the utilization efficiency of distributed computing resources. The additional capacity will also enable support for more projects with basic biological research relevance. This RAPID award to Washington University in Saint Louis is made by the Division of Biological Infrastructure using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

SARS-CoV-2病毒利用多种蛋白质感染人体细胞，逃避免疫反应，并自我复制。这些蛋白质具有对其功能至关重要的活动部分。了解蛋白质移动和改变构象的方式将为病毒生物学提供新的见解，并可能揭示新的治疗机会。获得该奖项的研究人员正在使用Folding@home分布式计算机模拟SARS-COV-2蛋白质，该计算机汇集了全球志愿公民科学家的计算资源，在个人计算机上进行模拟。由于巨大的公众兴趣和与主要技术公司非常富有成效的互动，Folding@home网络现在提供了超过2300万个CPU内核和60万个gpu的访问，使该网络比世界上最快的传统超级计算机强大大约10倍。该奖项的支持将为有效利用这一前所未有的计算资源所需的网络基础设施提供急需的升级，并与目前参与努力更好地了解SARS-COV-2的数百万人进行富有成效的接触。研究成果将发表在同行评议的期刊上，在科学会议上展示，并通过社交媒体和大众媒体广泛传播。Folding@home是世界上最大和最成功的分布式计算项目之一。目前对SARS-COV-2的研究工作包括对每种病毒蛋白的动态分析和对5万多种小分子相互作用的自由能扰动建模，以确定可能的治疗起点。寻找隐藏的结合位点是这项工作的主要重点，早期的结果是有希望的。在该奖项的支持下，将对Folding@home TCP/IP堆栈、工作收集服务器和后端分析服务器进行改进，以提高分布式计算资源的利用效率。额外的能力还将支持更多与基础生物学研究有关的项目。这项授予圣路易斯华盛顿大学的RAPID奖是由生物基础设施部利用《冠状病毒援助、救济和经济安全（CARES）法案》的资金颁发的。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential.

• DOI: 10.1016/j.bpj.2021.03.024
• 发表时间: 2021-07-20
• 期刊: Biophysical journal
• 影响因子: 3.4
• 作者: Vithani N;Ward MD;Zimmerman MI;Novak B;Borowsky JH;Singh S;Bowman GR
• 通讯作者: Bowman GR

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome.

• DOI: 10.1038/s41557-021-00707-0
• 发表时间: 2021-07
• 期刊: Nature chemistry
• 影响因子: 21.8
• 作者: Zimmerman MI;Porter JR;Ward MD;Singh S;Vithani N;Meller A;Mallimadugula UL;Kuhn CE;Borowsky JH;Wiewiora RP;Hurley MFD;Harbison AM;Fogarty CA;Coffland JE;Fadda E;Voelz VA;Chodera JD;Bowman GR
• 通讯作者: Bowman GR