The accuracy of protein structures in solution determined by AlphaFold and NMR

By N. Fowler, M. Williamson. 2022

97 citations recorded by the source corpus.

In the recent CASP (Critical Assessment of Structure Prediction) competition, AlphaFold2 performed outstandingly. Its worst predictions were for NMR structures, which has two alternative explanations: either the NMR structures were poor, implying that AlphaFold may be more accurate than NMR; or there is a genuine difference between crystal and solution structures. Here, we use the program ANSURR, which measures the accuracy of solution structures, and show that one of the NMR structures was indeed poor. We then compare AlphaFold predictions to NMR structures, and show that AlphaFold tends to be more accurate than NMR ensembles, in particular correctly more rigid in loops. There are however some cases where the NMR ensembles are more accurate. These tend to be dynamic structures where AlphaFold had low confidence. We suggest that AlphaFold could be used as the model for NMR structure refinements, and that AlphaFold structures validated by ANSURR require no further refinement.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Yi Zhao
2. Zhenyu Yang
3. Runsheng Chen
4. Xiaoxi Zeng

In Molecular Biology

1. Yi Zhao
2. Zhenyu Yang
3. Runsheng Chen
4. Xiaoxi Zeng
5. A. Bax
6. Yang Shen

Citations in the corpus

• AlphaFold2 and its applications in the fields of biology and medicine (2023, background): “68,69 Typically, the de novo structure determination of domains or proteins using NMR, which is time-consuming, may be replaced by the AF2 structures.”
• Predicting protein flexibility with AlphaFold (2023, background): “46 It was found that, the AF2 structures are generally more accurate than the NMR structural ensembles except for highly dynamic proteins or protein regions.”