Learn/Predict a structure

Read the confidence

Every prediction carries its own estimate of where it is wrong. Three readings cover most of it: pLDDT, a per-residue confidence drawn on the structure and along the sequence; PAE, a per-pair error that says whether two parts are placed right relative to each other; and one or two numbers that summarise them for the whole chain or the whole complex.

The ectodomain by ESMFold, coloured by confidence

pLDDT ≥ 90 · very high confidence
70 to 89 · confident
50 to 69 · low confidence
below 50 · very low confidence

No sequence loaded.

90 and above: Very high. Backbone and side chains can be trusted.
70 to 90: Confident. The backbone is right; side chains may not be.
50 to 70: Low. Treat with care.
Below 50: Very low. Usually disorder, a region with no fixed structure, rather than a wrong fold.

Where the parts sit

Each dark square on the diagonal is a domain the model is sure of on its own. The blocks between them say whether the domains are placed right against each other: dark is trusted, pale is not. Three confident domains with pale blocks between them means each fold is right and the arrangement is a guess.

Hover the grid to read the error between any two residues.

The numbers, and their thresholds

Metric	ESMFold	AlphaFold 2
pLDDT	73.56	92.67
pTM	0.8944	0.92
iPAE	7.235 Å	5.362 Å

pLDDT: Mean per-residue confidence of the predicted complex.
pTM: Predicted TM-score of the whole complex.
ipTM: Predicted TM-score of the interface alone.
iPAE: Mean predicted aligned error across the interface.

Two predictions of the same chain: ESMFold from the sequence alone, AlphaFold 2 with its alignment. For a complex, ipTM above 0.8 means the chains are placed reliably and below 0.5 means they are not; between the two, sample more before deciding.

pLDDT ≥ 90 · very high confidence
70 to 89 · confident
50 to 69 · low confidence
below 50 · very low confidence

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