+ with + predicted alignment error shown for Human +
+ from https://alphafold.ebi.ac.uk/entry/Q99814 +
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 Angstroms) between the modelled position and the pair of residues' real relative position.
-- Jalview visualises PAE matrices as an alignment annotation track, shaded from dark green to white, as used on the EBI-AlphaFold website (see ) -
+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.
++ Jalview visualises PAE matrices as an alignment annotation track, + shaded from dark green to white, similar to the encoding used on the + EBI-AlphaFold website (see O04090 3D model + at EBI-AlphaFoldDB). +
+
+
+ Importing PAE Matrices
@@ -45,8 +71,8 @@ PAE matrices using a pipeline such as ColabFold, then you can load them both together via the Load PDB - File dropdown menu in the 3D structure chooser. in a supported PAE format. + File dropdown menu in the 3D structure chooser, providing it is in a + supported PAE format.The Command Line @@ -55,22 +81,108 @@ annotated with PAE matrices and PLDDT scores.
- See Working with PAE - Matrices for information on how they are visualised and analysed in - Jalview. + Showing PAE Matrix Annotations +
++ When viewing 3D structures from the EBI-AlphaFold database or local 3D + structures with an associated PAE file, the PAE is imported as Reference + Annotation, which is not always automatically added to the alignment + view.
+To show the PAE, right click the sequence and locate the 'Add + Reference Annotation' entry in the Sequence ID submenu, or select all + sequences and locate the option in the Selection submenu. You can do + this in any alignment window (or view) where a sequence with + associated PAE data appears.
++ Adjusting the height of PAE matrix annotations +
++ PAE annotations behave in the same way as Jalview's line graph and + histogram tracks. Click+dragging up and down with the left (select) + mouse button held down will increase or decrease the height of the + annotation. You can also hold down SHIFT + whilst doing this to adjust the height of all PAE rows at once.
+PAE matrix annotation rows behave like any other sequence + associated annotation, with the following additional features:
+PAE matrices are useful for identifying regions of 3D structure + predictions that are likely to be positioned in space in the same or + similar way as shown in the predicted structure data. Regions of low + PAE often correlate with high alphafold reliability (PLDDT) scores, + but also complement them since they highlight well-folded regions such + as domains, and how well those regions have been predicted to be + positioned relative to eachother, which is important when evaluating + whether domain-domain interactions or other contacts can be trusted.
+To make it more easy to identify regions of low PAE, Jalview can + cluster the PAE matrix, allowing columns of the matrix to be grouped + according to their similarity, using an Average Distance (UPGMA) tree + algorithm and the sum of differences between each column's PAE values.
++ distij = ∥ pi-pj + ∥ +
++ To create a PAE matrix tree, right click on a PAE annotation's label + to open the annotation popup menu, and select Cluster + Matrix. Once the calculation has finished, a tree viewer will open, + and columns of the matrix are then partitioned into groups such that + the third left-most node from the root is placed in its own group. + Colours are randomly assigned to each group, and by default these will + also be overlaid on the matrix annotation row. +
+
- An additional Predicted Alignment Error file can also be - provided when importing 3D structure data. Jalview supports import of - PAE Matrices provided as AlphaFold - format JSON files - which are also produced by ColabFold. See Working with PAE Matrices for details on - what Jalview allows you to do with associated PAE matrix data. + PAE matrices and Jalview Projects
+Any PAE matrices imported to Jalview are saved along side any + trees and clustering defined on them in Jalview Projects.
- The Structure Chooser interface was introduced in Jalview - 2.9. + Support for visualision and analysis of predicted alignment + error matrices was added in Jalview 2.11.3.