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 radio buttons below), the N-terminal domain is well-defined in isolation. It is the relative domain orientation that is not well predicted. | 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 radio buttons below), the N-terminal domain is well-defined in isolation. It is the relative domain orientation that is not well predicted. | ||
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| + | <scene name='92/920232/Two_dimensional_200/1'>Residue 200</scene> | ||
<scene name='92/920232/Two_dimensional_400/1'>Residue 400</scene> | <scene name='92/920232/Two_dimensional_400/1'>Residue 400</scene> | ||
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| - | <scene name='92/920232/Two_dimensional_660/1'>Residue 660</scene> | ||
<scene name='92/920232/Two_dimensional_600/1'>Residue 600</scene> | <scene name='92/920232/Two_dimensional_600/1'>Residue 600</scene> | ||
| + | |||
| + | <scene name='92/920232/Two_dimensional_660/1'>Residue 660</scene> | ||
<scene name='92/920232/Two_dimensional_800/1'>Residue 800</scene> | <scene name='92/920232/Two_dimensional_800/1'>Residue 800</scene> | ||
Revision as of 15:00, 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
