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Folding@home:超过 20 年的公民科学成就预示着 exascale 时代的到来。

Folding@home: Achievements from over 20 years of citizen science herald the exascale era.

机构信息

Department of Chemistry, Temple University, Philadelphia, Pennsylvania.

Andreessen Horowitz, Menlo Park, California.

出版信息

Biophys J. 2023 Jul 25;122(14):2852-2863. doi: 10.1016/j.bpj.2023.03.028. Epub 2023 Mar 21.

Abstract

Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over 20 years, the Folding@home distributed computing project has pioneered a massively parallel approach to biomolecular simulation, harnessing the resources of citizen scientists across the globe. Here, we summarize the scientific and technical advances this perspective has enabled. As the project's name implies, the early years of Folding@home focused on driving advances in our understanding of protein folding by developing statistical methods for capturing long-timescale processes and facilitating insight into complex dynamical processes. Success laid a foundation for broadening the scope of Folding@home to address other functionally relevant conformational changes, such as receptor signaling, enzyme dynamics, and ligand binding. Continued algorithmic advances, hardware developments such as graphics processing unit (GPU)-based computing, and the growing scale of Folding@home have enabled the project to focus on new areas where massively parallel sampling can be impactful. While previous work sought to expand toward larger proteins with slower conformational changes, new work focuses on large-scale comparative studies of different protein sequences and chemical compounds to better understand biology and inform the development of small-molecule drugs. Progress on these fronts enabled the community to pivot quickly in response to the COVID-19 pandemic, expanding to become the world's first exascale computer and deploying this massive resource to provide insight into the inner workings of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and aid the development of new antivirals. This success provides a glimpse of what is to come as exascale supercomputers come online and as Folding@home continues its work.

摘要

生物分子的模拟具有极大的潜力,可以帮助我们理解生物学,但需要极其苛刻的计算。20 多年来,Folding@home 分布式计算项目开创了一种大规模并行的生物分子模拟方法,利用全球公民科学家的资源。在这里,我们总结了这一视角所带来的科学和技术进步。正如项目名称所暗示的,Folding@home 的早期重点是通过开发捕获长时间尺度过程的统计方法并促进对复杂动态过程的理解,推动我们对蛋白质折叠的理解取得进展。成功为拓宽 Folding@home 的范围奠定了基础,以解决其他功能相关的构象变化,如受体信号转导、酶动力学和配体结合。持续的算法进步、硬件发展,如基于图形处理单元 (GPU) 的计算,以及 Folding@home 的规模不断扩大,使该项目能够专注于大规模并行采样可以产生影响的新领域。虽然之前的工作试图扩展到具有较慢构象变化的更大蛋白质,但新的工作侧重于不同蛋白质序列和化学化合物的大规模比较研究,以更好地理解生物学并为小分子药物的开发提供信息。在这些方面的进展使社区能够迅速应对 COVID-19 大流行,扩展成为世界上第一台 exascale 计算机,并部署这一巨大资源,以深入了解严重急性呼吸系统综合征冠状病毒 2 (SARS-CoV-2) 病毒的内部工作原理,并帮助开发新的抗病毒药物。随着 exascale 超级计算机的上线以及 Folding@home 继续开展工作,这一成功提供了未来的一瞥。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/21b8/10398258/758fbba925f3/gr1.jpg

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