- <p>Predicted Alignment Error (PAE) matrices are produced by
- deep-learning based 3D-structure prediction pipelines such as
- AlphaFold. They reflect how reliably two parts of a model have been
- positioned in space, by giving for each residue the likely error (in
- Ångstroms) between that residue and every other modelled
- position the pair of residues' real relative position, if the model
- and real 3D structure were superimposed at that residue.</p>
+ <p>Predicted Alignment Error (PAE) matrices are produced by
+ deep-learning based 3D-structure prediction pipelines such as
+ AlphaFold. They reflect how reliably two parts of a model have been
+ positioned in space. Each column in a PAE matrix corresponds to a
+ residue in the model, and each gives the likely RMS error (in
+ Ångstroms) between that residue and every other modelled
+ position the pair of residues' real relative position, if the model
+ and real 3D structure were superimposed at that residue.</p>