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Tool: AlphaFold

AlphaFold is an artificial intelligence method for predicting protein structures that has been highly successful in recent tests. The method is described in:

Highly accurate protein structure prediction with AlphaFold. Jumper J, Evans R, Pritzel A, et al. Nature. 2021 Aug;596(7873):583-589.
Protein complex prediction with AlphaFold-Multimer. Evans R, O'Neill M, Pritzel A, et al. bioRxiv 2021.

The ChimeraX AlphaFold tool:

AlphaFold-predicted structures vary in confidence levels (see coloring) and should be interpreted with caution. The related tool AlphaFold Error Plot plots residue-residue alignment errors for AlphaFold structures.

The AlphaFold tool is also implemented as the alphafold command. Several ChimeraX presentations and videos show modeling with AlphaFold and related analyses. See also: Blast Protein, Modeller Comparative, Model Loops, Rotamers

AlphaFold Dialog
AlphaFold Coloring Dialog
AlphaFold Error Plot

AlphaFold Dialog

The AlphaFold tool can be opened from the Structure Prediction section of the Tools menu and manipulated like other panels (more...).

The Sequence can be specified by UniProt name or accession number, pasted in as plain text, or chosen from the menu of currently open protein structure chains.

For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains), or individually within a comma-separated list of UniProt identifiers or pasted-in amino acid sequences. Prediction may only be feasible for smaller complexes (details...).

AlphaFold Coloring Dialog

Clicking the Coloring button on the main AlphaFold tool shows the AlphaFold Coloring dialog for applying different color schemes to the predicted structures, as well as hiding, showing, and selecting their residues based on attribute value.

When first opened, AlphaFold-predicted structures are automatically colored by the pLDDT confidence measure in the B-factor field:

...in other words, using

color bfactor palette alphafold

The Color Key graphical interface or a command can be used to draw a corresponding color key, for example:

key red:low orange: yellow: cornflowerblue: blue:high  [other-key-options]

In the AlphaFold Coloring dialog, the Residues to act on are specified by using the menus to choose an AlphaFold-predicted model and one of the following:

Buttons act on the designated residues:

The AlphaFold Coloring dialog does not color continuously along a gradient to show the attribute values. For coloring along a gradient, see the commands color bfactor (for the confidence value, which is read from the B-factor field of the PDB file) and color byattribute (for other numerical attributes).

AlphaFold Error Plot

Besides the per-residue pLDDT confidence measure, AlphaFold gives for each pair of residues (X,Y) the expected position error at residue X if the predicted and true structures were aligned on residue Y. These residue-residue “predicted aligned error” or PAE values can be shown with AlphaFold Error Plot, which can be opened from the Structure Prediction section of the Tools menu and manipulated like other panels (more...). See also: the AlphaFold Error Estimates example and video, alphafold contacts

Choosing the corresponding AlphaFold structure from the menu of open atomic models associates it with the plot. This association allows coloring the structure as described below, and for selections on the plot to highlight the corresponding parts of the structure.

The PAE values can be either:

The PAE plot can also be shown by clicking the Error plot button on the AlphaFold dialog or by using the command alphafold pae, or the command alphafold fetch or alphafold match with the option pae true.

When the mouse cursor is over the plot, the residue pair and PAE value at its current position are reported in the bottom right corner of the window.

Clicking Color PAE Domains clusters the residues into coherent domains (sets of residues with relatively low PAE values) and uses randomly chosen colors to distinguish these domains in the structure (details...). Clicking Color pLDDT returns the structure to the default confidence coloring.

The plot's context menu includes:

The Color Key graphical interface or a command can be used to draw (in the main graphics window) a color key for the PAE plot. For example, to make a color key that matches the pae or paegreen scheme, respectively:

key pae :0 : : :15 : : :30  showTool true
key paegreen :0 : : :15 : : :30  showTool true

A title for the color key (e.g., “AlphaFold Predicted Aligned Error (Å)”) would need to be created separately with 2dlabels.


UCSF Resource for Biocomputing, Visualization, and Informatics / July 2022