Foldy: An open-source web application for interactive protein structure analysis

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 is a cloud-based application that enables scientists to use AI-based structural biology tools such as AlphaFold and DiffDock without software expertise. With many different deployment options, it can be set up by individuals, labs, universities, and companies in the cloud with no need for hardware resources. Foldy can predict the structure of proteins and complexes up to 6000 amino acids, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. Some structures are visible to the public on the Lawrence Berkeley Labs Foldy instance, and can be viewed at https://foldy.lbl.gov.Our manuscript highlights the user interface, deployment options, relative strengths of Foldy compared to existing tools, and some past applications of Foldy. It's an accessible solution for researchers who are not software experts. Many deployment options are possible and we highlight two: one of which can be set up in minutes, and the other can handle the traffic of thousands of users and hundreds of thousands of protein structures and docked ligands. This makes advanced AI-based tools more widely available, paving the way for accelerating life science research.By developing an easy-to-use platform, our work demonstrates that even computationally expensive AI-based tools like AlphaFold can be made accessible to a wide audience. Improvements in the accessibility of computational tools will allow more biologists to more easily apply computational tools to more problems. We are hopeful that Foldy addresses the growing need of making revolutionary computational tools accessible to more researchers.