Alphafold2

Title: AlphaFold2: A role for disordered protein prediction.

Authors: Carter J. Wilson, Wing-Yiu Choy, Mikko Karttunen

Abstract: The development of AlphaFold2 was a paradigm-shift in the structural biology community; herein we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that a naive use of Dictionary of Secondary Structure of Proteins (DSSP) to separate ordered from disordered regions leads to a dramatic overestimation in disorder content, and that the Predicted Aligned Error (PAE) provides a much more rigorous metric. In addition, we show that even when used for disorder prediction, conventional predictors can outperform the PAE in disorder identification, and note an interesting relationship between the PAE and secondary structure that may explain our observations and hints at a broader application of the PAE to IDP dynamics.