AlphaFold pLDDT and expected distance error
From Proteopedia
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==Expected distance error== | ==Expected distance error== | ||
| - | Alphafold also predicts the expected error in the distance of two residues. Thus, this is a 2-dimensional (pairwise) data set. The plot of the data is shown below. On the right, you can see the <scene name='92/920232/Two_dimensional/1'>expected error in the distance between residue 1000</scene> mapped by color on the second residue. It becomes apparent that the distance between residue 1000 and residues in the N-terminal part of the protein are ill-defined. However, if you show the expected errors to residue 400 (by using the | + | Alphafold also predicts the expected error in the distance of two residues. Thus, this is a 2-dimensional (pairwise) data set. The plot of the data is shown below. On the right, you can see the <scene name='92/920232/Two_dimensional/1'>expected error in the distance between residue 1000</scene> mapped by color on the second residue. If you hover over the residue, it will show the estimated distance error. It becomes apparent that the distance between residue 1000 and residues in the N-terminal part of the protein are ill-defined. However, if you show the expected errors to residue 400 (by using the links below), the N-terminal domain is well-defined in isolation. It is the relative domain orientation that is not well predicted. If you explore some other of the residues provided below, you will discover that there are subdomains within the N-terminal as well as the C-terminal domain. This is [[Methionine synthase|experimentally supported]]. |
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<script> script "/wiki/images/c/c8/Res800.spt"</script> | <script> script "/wiki/images/c/c8/Res800.spt"</script> | ||
| - | <text> | + | <text>Residue 800</text> |
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Revision as of 16:10, 18 August 2022
AlphaFold provides two measures of coordinate error. The residue-by-residue pLDDT value stored directly in the coordinate file, and the pairwise residue distance error stored in a separate file.
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- ↑ Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics. 2013 Nov 1;29(21):2722-8. doi: 10.1093/bioinformatics/btt473., Epub 2013 Aug 27. PMID:23986568 doi:http://dx.doi.org/10.1093/bioinformatics/btt473
