Portal

I previously summarized some debate around a method called AF-Cluster (see the post here: https://portal.valencelabs.com/ml-for-proteins/post/active-scientific-debate-on-generating-conformations-with-alphafold-KbrktEWEf7S60TC) Now, Wayment-Steele and co-authors respond to concerns about reproducibility with a new preprint, arguing that the critiques used older AF2 params that weren't directly comparable with what they were using. They even provide a new colab notebook to help the field compare and combine sampling methods. This seems like a nice response to reproducibility to me; trying to be transparent and developing resources to help bridge divides. https://www.biorxiv.org/content/10.1101/2024.07.29.605333 There have been a few papers recently addressing the huge resources needed for training protein language models (PLMs) and proposing solutions. Nathan Frey and a group at Genentech discussed "Cramming Protein Language Model Training in 24 GPU Hours", training a model in a single d

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• Lauren Pearson