# Four-panel figure: a predicted protein structure and its confidence

> A structure-prediction figure: the predicted model coloured by confidence, the per-residue pLDDT along the sequence, the predicted aligned error (PAE) map that shows which domains are placed confidently, and the predicted contact map.

- Page: https://www.labcanvas.com/templates/multipanel/four-panel-figure-predicted-protein-structure-confidence
- Open in the LabCanvas editor (LabCanvas account): https://www.labcanvas.com/editor.html?template=multipanel-protein-structure-prediction
- Updated: 2026-10-14
- Category: Multipanel figures
- Method: Worked examples
- Product: A 2 × 2 figure (a–d) for a structure-prediction result
- Key result: Synthetic example traces from the Graph app’s science presets; confidence bands as in the AlphaFold Database
- Figure: 672.76 × 393.5 px, 26 editable layers (1 generated objects with settings)

## Steps

1. **a · Model**: The predicted structure coloured by pLDDT
2. **b · pLDDT**: Confidence per residue with the AlphaFold Database bands (> 90, 70–90, 50–70, < 50)
3. **c · PAE**: Expected position error between residue pairs: low-error blocks are confidently placed domains
4. **d · Contacts**: Residue pairs predicted to be close

## Strengths

- The standard way to report a predicted model
- Every graph editable

## Limitations

- Example values only

## Uses

- Structural biology papers
- Protein design and engineering

## References

1. Jumper et al., “Highly accurate protein structure prediction with AlphaFold”, Nature 2021. https://doi.org/10.1038/s41586-021-03819-2 (primary)
2. Varadi et al., “AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models”, Nucleic Acids Res. 2022. https://doi.org/10.1093/nar/gkab1061 (primary)
3. Rougier, Droettboom & Bourne, “Ten simple rules for better figures”, PLoS Comput. Biol. 2014. https://doi.org/10.1371/journal.pcbi.1003833 (review)

Credit: Example data generated for this template. After Jumper et al., Nature 2021 and Varadi et al., Nucleic Acids Res. 2022.

## Questions

**What does the “Four-panel figure: a predicted protein structure and its confidence” template show?** A structure-prediction figure: the predicted model coloured by confidence, the per-residue pLDDT along the sequence, the predicted aligned error (PAE) map that shows which domains are placed confidently, and the predicted contact map.

**What are the steps shown in “Four-panel figure: a predicted protein structure and its confidence”?** 1. a · Model: The predicted structure coloured by pLDDT. 2. b · pLDDT: Confidence per residue with the AlphaFold Database bands (> 90, 70–90, 50–70, < 50). 3. c · PAE: Expected position error between residue pairs: low-error blocks are confidently placed domains. 4. d · Contacts: Residue pairs predicted to be close.

**Which papers is “Four-panel figure: a predicted protein structure and its confidence” based on?** Jumper et al., “Highly accurate protein structure prediction with AlphaFold”, Nature 2021 (doi:10.1038/s41586-021-03819-2); Varadi et al., “AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models”, Nucleic Acids Res. 2022 (doi:10.1093/nar/gkab1061); Rougier, Droettboom & Bourne, “Ten simple rules for better figures”, PLoS Comput. Biol. 2014 (doi:10.1371/journal.pcbi.1003833).

**Can I edit the “Four-panel figure: a predicted protein structure and its confidence” template?** Yes. Open it in the LabCanvas editor: all 26 layers are editable, including 1 generated objects (structures, plots, equipment) with their own settings. Change the text, colours and layout, then export PNG, TIFF, SVG or PDF.

**Do I need an account to use this template?** Not to view it here. To open and edit it, sign in to LabCanvas or create a free account (the free plan keeps up to 3 designs). Downloading the figure is part of LabCanvas Pro (US$19 a month or US$199 a year).