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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.<\/jats:p>\n<jats:p>In our manuscript, we detail Foldy\u2019s 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\u2019s 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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011171","type":"journal-article","created":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T18:35:00Z","timestamp":1706898900000},"page":"e1011171","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Foldy: An open-source web application for interactive protein structure analysis"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7564-1708","authenticated-orcid":true,"given":"Jacob B.","family":"Roberts","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0172-4145","authenticated-orcid":true,"given":"Alberto A.","family":"Nava","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5383-4944","authenticated-orcid":true,"given":"Allison N.","family":"Pearson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew R.","family":"Incha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis E.","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melody","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abhay","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1490-8074","authenticated-orcid":true,"given":"Jay D.","family":"Keasling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,2,2]]},"reference":[{"key":"pcbi.1011171.ref001","first-page":"1","article-title":"Highly accurate protein structure prediction with AlphaFold","author":"J Jumper","year":"2021","journal-title":"Nature"},{"key":"pcbi.1011171.ref002","first-page":"eabj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","author":"M Baek","year":"2021","journal-title":"Science"},{"key":"pcbi.1011171.ref003","article-title":"Protein complex prediction with AlphaFold-Multimer","author":"R Evans","year":"2021","journal-title":"bioRxiv"},{"key":"pcbi.1011171.ref004","article-title":"Evolutionary-scale prediction of atomic level protein structure with a language model","author":"Z Lin","year":"2022","journal-title":"bioRxiv"},{"issue":"6604","key":"pcbi.1011171.ref005","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1126\/science.abn2100","article-title":"Scaffolding protein functional sites using deep learning","volume":"377","author":"J Wang","year":"2022","journal-title":"Science"},{"issue":"6573","key":"pcbi.1011171.ref006","doi-asserted-by":"crossref","first-page":"eabm4805","DOI":"10.1126\/science.abm4805","article-title":"Computed structures of core eukaryotic protein complexes","volume":"374","author":"IR Humphreys","year":"2021","journal-title":"Science"},{"issue":"6","key":"pcbi.1011171.ref007","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"M Mirdita","year":"2022","journal-title":"Nat Methods"},{"issue":"7873","key":"pcbi.1011171.ref008","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41586-021-03828-1","article-title":"Highly accurate protein structure prediction for the human proteome","volume":"596","author":"K Tunyasuvunakool","year":"2021","journal-title":"Nature"},{"key":"pcbi.1011171.ref009","unstructured":"Predict protein structures with AlphaFold [Internet]. 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