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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 ChimeraX AlphaFold tool:

Users should cite:

Highly accurate protein structure prediction with AlphaFold. Jumper J, Evans R, Pritzel A, et al. Nature. 2021 Aug;596(7873):583-589.

...and for multimer prediction:

Protein complex prediction with AlphaFold-Multimer. Evans R, O'Neill M, Pritzel A, et al. bioRxiv 2021. doi: https://doi.org/10.1101/2021.10.04.463034.

The AlphaFold Database contains modeled structures for protein sequences in UniProt:

...and is described in:

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Varadi M, Anyango S, Deshpande M, et al. Nucleic Acids Res. 2021 Nov 17:gkab1061. doi: 10.1093/nar/gkab1061.

The predicted structures vary in confidence levels and should be interpreted with caution. The database contains structures for single chains, not complexes; assembling the individual structures into a complex may give unphysical results where parts of the chains intersect or interact poorly with one another.

The AlphaFold tool is also implemented as the alphafold command. See also: Blast Protein, Modeller Comparative, Model Loops, AlphaFold vs. experiment, AlphaFold for cryoEM, AlphaFold for complexes, and ChimeraX videos:

Dialog and Buttons

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...).


UCSF Resource for Biocomputing, Visualization, and Informatics / December 2021