AlphaFold pLDDT and expected distance error

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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>
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<jmol>
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<jmolLink>
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<script> script "/wiki/images/d/d4/Res200.spt"</script>
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<text>Residue 200</text>
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</jmolLink>
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</jmol>
<jmol>
<jmol>
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</jmol>
</jmol>
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<scene name='92/920232/Two_dimensional_400/1'>Residue 400</scene>
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<jmol>
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<jmolLink>
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<script> script "/wiki/images/1/1c/Res400.spt"</script>
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<text>Residue 400</text>
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</jmolLink>
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</jmol>
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<scene name='92/920232/Two_dimensional_600/1'>Residue 600</scene>
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<jmol>
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<jmolLink>
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<script> script "/wiki/images/7/79/Res600.spt"</script>
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<text>Residue 600</text>
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</jmolLink>
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</jmol>
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<scene name='92/920232/Two_dimensional_660/1'>Residue 660</scene>
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<jmol>
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<jmolLink>
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<script> script "/wiki/images/6/6d/Res680.spt"</script>
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<text>Residue 680</text>
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</jmolLink>
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</jmol>
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<scene name='92/920232/Two_dimensional_800/1'>Residue 800</scene>
 
<scene name='92/920232/Two_dimensional/1'>Residue 1000</scene>
<scene name='92/920232/Two_dimensional/1'>Residue 1000</scene>

Revision as of 15:57, 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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  1. ↑ 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

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Karsten Theis, Eric Martz

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