FoldCompare
How close is an AlphaFold prediction to the experimental structure? Pick a protein below (or enter your own pair), and this tool fetches the experimental structure from the RCSB PDB and AlphaFold's prediction from the AlphaFold Database, superposes them, and reports the Cα RMSD, the per-residue divergence, and — honestly — whether the disagreement is meaningful or just where the model was unsure. Everything runs in your browser; nothing is installed and nothing about you is collected.
This is the tool — the core superposition + honest read-out. A native version, when it ships, adds a 3D divergence-painted overlay, a numerical stat table, saved comparisons, and offline use; it never gates the web.
Per-residue divergence
Distance (Å) between the aligned experimental and predicted Cα, residue by residue. Tall red bars mark where the two structures disagree most; faded bars mark residues AlphaFold predicted with low confidence (pLDDT < 70) — where a disagreement is ambiguous, because the model was unsure there too.
Split view
Methods & limits
- Alignment: rigid-body Kabsch superposition over matched Cα atoms (the same v1.0 algorithm as the native app), computed in your browser from the fetched coordinates.
- Residue matching is by number, within the experimental chain that best overlaps the prediction. There is no sequence realignment yet — if the two number their residues differently, coverage drops and the pair may not align. Coverage is reported honestly.
- Cα only. Side-chain, backbone-torsion, and all-atom differences are not measured; RMSD is over Cα, the standard backbone summary.
- Partial structures compare partially. A crystal of one domain, or one chain of an assembly, aligns only over the residues both structures share — the coverage percentage tells you how much.
- Predictions are models, not experiments. pLDDT colouring shows where AlphaFold was confident (blue) and where it was not (orange); the verdict weights divergence by that confidence.
About this tool
Experimental structures come from the RCSB Protein Data Bank; predictions from the AlphaFold Database (EMBL-EBI / Google DeepMind). Both are fetched directly by your browser and rendered with Mol* via PDBe Mol*, self-hosted here — no third-party CDN, no tracking, no server. AlphaFold DB data is released under CC BY 4.0; please cite the AlphaFold and RCSB PDB papers when you use a structure. This tool is part of the free, non-profit Fold Commons project.