Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.
Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Japan.
Commun Biol. 2024 Oct 14;7(1):1320. doi: 10.1038/s42003-024-07031-6.
Cryogenic electron microscopy (Cryo-EM) is a widely used technique for visualizing the 3D structures of many drug design targets, including membrane proteins, at atomic resolution. However, the necessary throughput for structure-based drug design (SBDD) is not yet achieved. Currently, data analysis is a major bottleneck due to the rapid advancements in detector technology and image acquisition methods. Here we show "GoToCloud", a cloud-computing-based platform for advanced data analysis and data management in Cryo-EM. With GoToCloud, it is possible to optimize computing resources and reduce costs by selecting the most appropriate parallel processing settings for each processing step. Our benchmark tests on GoToCloud demonstrate that parallel computing settings, including the choice of computational hardware, as well as a required target resolution have significant impacts on the processing time and cost performance. Through this optimization of a cloud computing environment, GoToCloud emerges as a promising platform for the acceleration of Cryo-EM SBDD.
低温电子显微镜（Cryo-EM）是一种广泛用于可视化许多药物设计靶标三维结构的技术，包括膜蛋白，达到原子分辨率。然而，基于结构的药物设计（SBDD）的必要通量尚未实现。目前，由于检测器技术和图像采集方法的快速发展，数据分析是一个主要的瓶颈。在这里，我们展示了“GoToCloud”，这是一个基于云计算的平台，用于 Cryo-EM 的高级数据分析和数据管理。使用 GoToCloud，可以通过为每个处理步骤选择最合适的并行处理设置来优化计算资源并降低成本。我们在 GoToCloud 上的基准测试表明，并行计算设置，包括计算硬件的选择，以及所需的目标分辨率，对处理时间和成本性能有重大影响。通过对云计算环境的这种优化，GoToCloud 成为加速 Cryo-EM SBDD 的有前途的平台。
