AlphaFold quickstart
Fetch a pre-computed AlphaFold structure by UniProt ID in 2-5 seconds, no GPU — pLDDT-colored canvas card, downloadable PDB, ESMFold fallback on a miss.
You want the 3D structure of a known protein and it is already in the AlphaFold Database — so instead of predicting it, you fetch it by UniProt ID (or protein name) in one step, and the pre-computed structure lands as a canvas card in 2-5 seconds with no GPU.
Fetch an AlphaFold structure
The fastest way to get a protein structure on the platform when the protein is in the AlphaFold Database.
In chat (recommended)
Just ask:
Fetch the AlphaFold structure for P00533
Or by protein name (the platform resolves to UniProt automatically):
Get the AlphaFold structure for human EGFR
The result lands as a canvas card with the 3D structure, pLDDT confidence coloring, and a download button for the PDB file.
Chat is the only way in
An AlphaFold Database fetch runs only inside a chat turn: there is no tool form, no job, and no CLI or MCP command for it. The one thing Ivy needs is a UniProt accession, or a protein name it can resolve to one.
Typical duration: 2-5 seconds for the HTTP round-trip + structure parsing. No GPU.
What happens if the protein isn't in the database
The fetch returns a "not found" result. To handle this gracefully, either:
- Chain in chat: "Try AlphaFold first; if it's not in the database, run ESMFold."
- Or ask Ivy to predict it with ESMFold from the UniProt sequence.
The AlphaFold DB covers ~200M proteins across most well-studied proteomes, so misses are rare for human / model-organism work — but common for novel synthetic sequences or fragments.
Next steps
After fetching a structure:
- Dock a ligand: "Now dock aspirin against this structure" → runs DiffDock
- Find binding pockets: "Find binding pockets" → runs P2Rank
- Refine for docking: "Add hydrogens and assign partial charges" → runs PDB2PQR
- Compare to experimental structure: "Is there a PDB structure for this protein?" → runs a PDB search
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