Graphical abstract template · Multipanel figures · Worked examples
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.
Updated 3 cited papers26 editable layers
At a glance
- 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 × 411.79 px (16:9), 26 editable layers, 1 generated objects
Step by step
- a · ModelThe predicted structure coloured by pLDDT
- b · pLDDTConfidence per residue with the AlphaFold Database bands (> 90, 70–90, 50–70, < 50)
- c · PAEExpected position error between residue pairs: low-error blocks are confidently placed domains
- d · ContactsResidue 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
Papers this template follows
- Jumper et al., “Highly accurate protein structure prediction with AlphaFold”, Nature 2021. doi:10.1038/s41586-021-03819-2primary
- 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/gkab1061primary
- Rougier, Droettboom & Bourne, “Ten simple rules for better figures”, PLoS Comput. Biol. 2014. doi:10.1371/journal.pcbi.1003833review
Example data generated for this template. After Jumper et al., Nature 2021 and Varadi et al., Nucleic Acids Res. 2022.
How templates are written and checked: editorial guidelines.
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).
