Methods

Protein structures were predicted using AplhaFold version 2.2.4 (Varadi et al., 2022). In addition to structure visualization, the following measures of accuracy are displayed on this page

• Predicted local distance difference test (pLDDT), an estimate how well (scale: 0-100) the prediction would agree with an experimental structure based on the local distance difference test Cα (lDDT-Cα)
• Predicted Template Modeling Score (pTM), a measures the structural congruence between two folded protein structures (scale: 0-1). AlphaFold2 allows the inclusion of PDB templates for modeling, as part of the modeling options. Although the templates are not required for predictions, they can improve model performance.
• Predicted Aligned Error (PAE), the expected positional error at residue x if the predicted and actual structures are aligned on residue y (using the Cα, N and C atoms), measured in Ångströms and capped at 31.75 Å.

References

1. Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021)
2. Varadi et al., (2022) AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Research, 50(D1): D439–D444

Please click on animated image to download the model file.