How to know when to trust AlphaFold2's protein structure predictions

What is it about?

AlphaFold2 generates typically accurate predictions of protein structures. However, it remains unclear whether AlphaFold2 can uniformly predict the wide spectrum of proteins equally well. In this paper, we conducted an in-depth analysis of AlphaFold2's fairness using data comprised of five million reported protein structures from its open-access repository.

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Why is it important?

Systematic investigation into the fairness and unbiased nature of AlphaFold2's predictions is still an area yet to be thoroughly explored. Many users of AlphaFold2 are not experts in deep learning, and this raises concerns regarding when to rely on AlphaFold2’s protein structure predictions. These concerns become more critical as AlphaFold2 is increasingly being used in structure-based drug design and protein functional research where misinterpretations could prove costly.