Protein structures
AlphaFold structure viewer
Search a protein by name or UniProt accession. The page loads the published AlphaFold DB model and draws it in the browser.
What the viewer loads
A name goes to UniProt. Reviewed entries are tried first. The matching accession is then requested from AlphaFold DB, and 3Dmol.js draws the model. Cartoon, stick, sphere, and surface are views of that same file.
Color follows the AlphaFold DB pLDDT legend: blue, cyan, yellow, orange. Read the legend on the viewer before you describe a loop or a domain as reliable.
Where a figure helps
- A results or methods panel that shows the fold you discuss.
- A check of low-confidence regions before a sentence treats them as structure.
- A starting PNG for a paper. The copied LaTeX block is a figure environment that needs graphicx.
How to get a structure on the page
1. Search
Type TP53, hemoglobin, insulin, or an accession such as P04637. The chips under the box load those examples.
2. Load
Wait for UniProt and AlphaFold DB. The status line names the accession that came back.
3. Turn the model
Drag to rotate. Switch Cartoon, Stick, Sphere, or Surface. The color stays on pLDDT.
4. Export
Download PNG or copy LaTeX. Insert into paper saves the PNG only when this page was opened with a project id.
Limits
- This page does not predict a new structure. It shows a model AlphaFold DB already has.
- pLDDT is model confidence. It is not a crystal or cryo-EM structure from the PDB.
- A common name can match the wrong protein. Use the accession in the status line.
- The PNG is the current view in the browser, not a ray-traced figure.
Questions
Does this page run AlphaFold?
No. It loads a structure that AlphaFold DB already published. If that database has no model for the accession, the viewer has nothing to draw.
What does the color mean?
Residues are colored by pLDDT, the model confidence score used by AlphaFold DB. Blue is very high, cyan is confident, yellow is low, and orange is very low. pLDDT is not an experimental structure from the PDB.
Can I search by protein name?
Yes. A name is sent to UniProt. The viewer prefers a reviewed entry, then any match, and loads that accession from AlphaFold DB. The status line shows which accession was used.
How do I put the structure in a paper?
Download PNG, or copy the LaTeX figure block. The block expects graphicx and an image file in the project. Insert into paper also saves the PNG when a Bibby project id is in the page address.
Put the fold next to the paragraph
Copy the figure block, add the PNG to the project, and compile. Bibby is the LaTeX editor around this viewer.
Start writing