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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 Jul 15. doi: 10.1038/s41586-021-03819-2.

The AlphaFold Database contains predictions for 21 species, including humans. It does not cover all of UniProt. The predicted structures vary in confidence levels and should be interpreted with caution. The AlphaFold system predicts structures for single chains, not complexes; assembling the individual predictions 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, comparing AlphaFold and experimental structures, and ChimeraX videos: searching by sequence for AlphaFold predictions (first 5 minutes), fetching an AlphaFold prediction, matching an assembly, predicting a new structure

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.

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