Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
PLoS Comput Biol. 2024 Feb 2;20(2):e1011171. doi: 10.1371/journal.pcbi.1011171. eCollection 2024 Feb.
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy's interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy's interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
Foldy 是一款基于云的应用程序，它允许非计算生物学家轻松地使用高级基于人工智能的结构生物学工具，包括 AlphaFold 和 DiffDock。它具有多种部署选项，可以在云端供个人、实验室、大学和公司使用，而无需硬件资源，也可以配置为利用本地可用的计算机。Foldy 使科学家能够使用 AlphaFold 预测长达 6000 个氨基酸的蛋白质和复合物的结构，可视化 Pfam 注释，并使用 AutoDock Vina 和 DiffDock 对接配体。在我们的论文中，我们详细介绍了 Foldy 的界面设计、部署策略以及针对各种用户场景的优化。我们通过案例研究展示了它的应用，包括合理的酶设计和分析具有未知功能域的蛋白质。此外，我们还将 Foldy 的界面和管理功能与该领域的其他开源和闭源工具进行了比较，说明了它在管理复杂数据和计算任务方面的实用性。我们的论文强调了 Foldy 作为生命科学研究人员日常工具的优势，并展示了 Foldy 如何使现代工具更易于访问和更高效。
