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Medium confidence is often close enough that you can formulate a hypothesis, but high confidence still isn't close enough that you'd stake millions of dollars o
by COGlory 4y ago
Medium confidence is often close enough that you can formulate a hypothesis, but high confidence still isn't close enough that you'd stake millions of dollars of experiments on it anyways. Most of the people in structural biology in pharma that I have chatted with said they're still solving the structures of their targets even with high-confidence AlphaFold models.
For me, as someone solving structures on a monthly basis, AlphaFold is great because after I get back my electron density map, I dump my sequence into AlphaFold, get a model (of any confidence) and most of it fits well enough into my density map that I don't have to start trying to model from nothing, and it saves me honestly days of work.
- siver_john 4y agoThat's a cool way I had never thought about it being used. Just for my own curiosity do you know if that is a common use case in the protein solving field? (I'd imagine it would also be useful in NMR experiments for getting initial point labels).
- flobosg 4y agoIt is quite common to use predicted models as an aid for phasing and molecular replacement; even Foldit models have been adopted for that purpose: https://www.nature.com/articles/nsmb.2119 https://www.nature.com/articles/nsmb.2119
- dekhn 4y agoWhat's really funny about using AlphaFold predictions to bootstrap a model into a density map is eventually, your structure, based on an AF prediction, will eventually be folded into the dataset used to train the next version of AlphaFold. Talk about test set/training set leakage!