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Figure 1
Prediction modes of AlphaFold2 and their relationships. This tree diagram shows how AlphaFold2 residues are divided into our modes, first by pLDDT, then by contact packing and then by validation outliers if necessary. Validation outliers are rare in high-pLDDT regions and are not used to define additional modes. For each mode, the name is listed, followed by the color used in our tool's kinemage markup, followed by the frequency of that mode within the human proteome predictions. In the kinemage, markup for each mode can be toggled individually to aid readability. Example markup is shown in Fig. 4[link].

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 81| Part 10| October 2025| Pages 558-572
https://doi.org/10.1107/S2059798325007843
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