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
- Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021)
- 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.