AlphaFold Fetch

AlphaFold is an artificial intelligence method for predicting protein structures. With the AlphaFold tool or command, ChimeraX can search for and load predicted structures from the freely available AlphaFold Database, automatically coloring them by confidence value:

• 100 to 90 – high accuracy
• 90 to 70 – backbone accuracy
• 70 to 50 – low confidence, caution
• 50 to 0 – should not be interpreted, may be disordered

The figure shows the predicted structure of UniProt entry TOM40_HUMAN, a channel protein needed to import other proteins into mitochondria. See the command file tom40.cxc for fetching data and other setup (background color, etc.).

Opening a sequence from UniProt also opens a dialog in which its annotations or “features” can be clicked to highlight those regions in both the sequence and the associated 3D structure. The low-confidence part of this structure (orange and red) maps to compositionally biased and likely disordered regions near the N-terminus of the sequence.

The architecture of the human ribosome has been determined at near-atomic resolution by electron microscopy (Anger et al., Nature 497:80 (2013)). The structure, comprising 82 proteins and five RNA molecules, is shown with shadows cast from all directions to accentuate depth. In the background are schematic representations of contacts between the component molecules.

See the image setup script card.cxc using the 'Tis the Season color palette (credit to MrsP). See also the RBVI holiday card gallery.

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