Class set · a printable
The Pitfall Card
Nine ways to over-read a predicted structure. Read a paper, a news story or a poster with the card beside you. Mark a square only when you can point to the figure or the line.
1
A very-low-confidence stretch drawn as if it were a solid, folded part.
Below pLDDT 50 the model is not placing that stretch with confidence. It may be flexible or disordered, which can be how the protein works.
Practise it: DisorderDuty
Where: ______________
2
Pale (low-confidence) parts treated as unimportant, or as the model failing.
Low confidence says how sure the model is about position, not whether a part matters.
Practise it: VanishPoint
Where: ______________
3
Two confident domains trusted in the arrangement shown, without checking the PAE plot.
Each domain can be very confident while the model is unsure how they sit relative to each other. That is what PAE shows.
Practise it: HingeHunt
Where: ______________
4
A missing metal, cofactor or partner chain ignored.
An AlphaFold DB model is one chain on its own: haem, zinc, ligands and partner chains are not in it.
Practise it: WhatsMissing
Where: ______________
5
One static model treated as the only shape the protein has.
A model is one picture. Real proteins move, and some switch between shapes.
Practise it: NotMarbles
Where: ______________
6
Side-chain positions over-read where confidence is only confident or lower.
Above pLDDT 90 side chains are often placed well; between 70 and 90 the backbone is usually right but side chains are less certain.
Practise it: NumberReader
Where: ______________
7
A figure of a predicted structure with no confidence colouring or note.
Show the pLDDT colours, or say in the caption how confident each part is.
Practise it: HonestReport
Where: ______________
8
"The structure" written where "the predicted structure" is meant.
Say prediction when it is a prediction; an experiment is a different kind of evidence.
Practise it: HonestReport
Where: ______________
9
A pocket in a model read as a measured binding site, or as how tightly a drug binds.
A pocket is a shape in a prediction. Whether and how tightly anything binds needs an experiment.
Practise it: PocketScout
Where: ______________
No square is a mistake in itself when the authors say what they mean: a model shown with its confidence, and called a prediction, is honest. The card is for reading carefully, not for scoring anyone.
Fold Commons · class set · updated 2026-10-04 · CC BY 4.0