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Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well\u2010known human amyloids, amyloid\u2010\u03b2 and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated \u03b2\u2010strand sheets forming a cross\u2010\u03b2 configuration. However, certain amphipathic \u03b1\u2010helical subunits can also form amyloid fibrils adopting a cross\u2010\u03b1 structure. Some AMPs in the study exhibited a combination of cross\u2010\u03b1 and cross\u2010\u03b2 amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored \u03b1\u2010helical structures in the tested amyloids, successfully predicting the presence of \u03b1\u2010helical mated sheets and a hydrophobic core resembling the cross\u2010\u03b1 configuration. This implies that the AI\u2010based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an \u03b1\u2010helical membrane\u2010active form of toxic peptides, which is triggered upon interaction with lipid membranes.<\/jats:p>","DOI":"10.1002\/prot.26618","type":"journal-article","created":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T06:35:21Z","timestamp":1697697321000},"page":"265-281","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["What can\n                    <scp>AlphaFold<\/scp>\n                    do for antimicrobial amyloids?"],"prefix":"10.1002","volume":"92","author":[{"given":"Peleg","family":"Ragonis\u2010Bachar","sequence":"first","affiliation":[{"name":"Department of Biology Technion\u2010Israel Institute of Technology  Haifa Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Axel","sequence":"additional","affiliation":[{"name":"George S. 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