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.
-
Residue <jmol>
+
<scene name='92/920232/Two_dimensional_400/1'>Residue 400</scene>
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<jmolRadioGroup>
+
 
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<item>
+
<scene name='92/920232/Two_dimensional_600/1'>Residue 600</scene>
-
<script>{*.ca}.property_t = [11, 8, 5, 5, 5, 5, 5, 4, 4, 4, 5, 4, 4, 4, 5, 5, 4, 4, 4, 5, 5, 5, 5, 6, 6, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6, 6, 6, 6, 7, 6, 6, 6, 6, 6, 6, 6, 6, 5, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 5, 5, 6, 5, 5, 5, 6, 5, 5, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 5, 4, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 4, 3, 3, 3, 2, 2, 2, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 4, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 4, 4, 4, 5, 4, 4, 4, 4, 3, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 6, 5, 5, 5, 6, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 0, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 2, 2, 3, 3, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 4, 4, 5, 4, 5, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 2, 2, 3, 3, 2, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 4, 4, 3, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 6, 5, 5, 5, 6, 6, 6, 8, 10, 13, 14, 17, 19, 22, 19, 21, 23, 23, 23, 25, 25, 27, 26, 25, 26, 26, 27, 27, 24, 25, 24, 25, 23, 24, 23, 23, 21, 21, 23, 25, 26, 26, 24, 27, 27, 26, 26, 26, 27, 27, 28, 27, 26, 28, 28, 28, 28, 28, 28, 26, 27, 26, 26, 26, 24, 27, 25, 27, 25, 25, 25, 23, 24, 23, 23, 23, 24, 21, 22, 21, 22, 21, 22, 21, 22, 24, 21, 22, 25, 25, 23, 25, 25, 24, 25, 26, 27, 27, 27, 27, 28, 27, 28, 28, 28, 28, 29, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 28, 27, 28, 27, 28, 27, 27, 24, 26, 26, 24, 24, 27, 27, 26, 26, 27, 27, 26, 27, 27, 28, 28, 28, 28, 27, 28, 28, 28, 27, 28, 26, 29, 28, 27, 28, 28, 27, 28, 29, 28, 28, 28, 27, 29, 28, 28, 27, 27, 26, 26, 27, 26, 26, 28, 26, 28, 27, 28, 27, 27, 27, 27, 27, 28, 28, 28, 29, 28, 28, 28, 27, 29, 28, 28, 28, 27, 27, 25, 26, 26, 26, 26, 26, 26, 25, 27, 27, 27, 28, 28, 25, 26, 28, 28, 27, 28, 28, 28, 28, 27, 27, 27, 26, 25, 24, 26, 27, 25, 26, 27, 27, 27, 28, 28, 28, 28, 29, 29, 27, 28, 28, 28, 27, 27, 28, 28, 27, 26, 27, 27, 27, 26, 26, 26, 25, 27, 27, 27, 27, 27, 26, 27, 27, 27, 25, 27, 27, 27, 28, 28, 27, 29, 27, 28, 28, 28, 27, 28, 28, 29, 27, 29, 28, 30, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 29, 28, 29, 29, 29, 30, 29, 29, 28, 29, 29, 29, 28, 28, 28, 28, 27, 26, 27, 25, 25, 25, 25, 24, 24, 25, 24, 24, 26, 25, 25, 25, 25, 26, 25, 24, 24, 23, 22, 22, 22, 24, 25, 24, 24, 25, 25, 25, 27, 26, 27, 26, 26, 28, 27, 28, 28, 28, 29, 29, 29, 28, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 30, 29, 28, 29, 28, 29, 28, 28, 27, 28, 29, 28, 29, 29, 28, 29, 29, 28, 29, 28, 28, 29, 29, 29, 29, 28, 29, 27, 27, 28, 28, 28, 27, 27, 27, 27, 28, 27, 29, 28, 27, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 28, 28, 28, 28, 29, 28, 28, 28, 29, 29, 29, 27, 28, 29, 29, 28, 27, 28, 28, 28, 27, 28, 27, 27, 27, 27, 27, 27, 26, 27, 27, 25, 26, 28, 26, 25, 26, 28, 26, 26, 28, 28, 26, 28, 29, 28, 27, 29, 29, 28, 29, 29, 30, 29, 29, 29, 29, 29, 29, 29, 29, 28, 29, 29, 27, 27, 29, 27, 26, 27, 26, 28, 28, 28, 28, 27, 26, 27, 25, 27, 27, 26, 26, 28, 27, 26, 28, 27, 28, 28, 27, 28, 29, 29, 29, 28, 29, 29, 28, 29, 29, 28, 29, 29, 29, 29, 28, 29, 29, 28, 28, 28, 28, 28, 29, 28, 27, 26, 27, 26, 27, 27, 28, 29, 28, 29, 28, 29, 28, 27, 27, 26, 28, 26, 27, 27, 27, 28, 29, 28, 28, 28, 29, 28, 29, 29, 29, 28, 29, 29, 28, 29, 29, 30, 29, 29, 29, 29, 28, 28, 28, 28, 27, 29, 28, 28, 28, 27, 28, 27];
+
 
-
select alpha; color "bwr"; color property_t; spacefill off; label off;
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<scene name='92/920232/Two_dimensional_800/1'>Residue 800</scene>
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set hoverlabel "residue %r vs 400: %[property_t] \u00c5";
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select 400 and alpha; spacefill on; color yellow;
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<scene name='92/920232/Two_dimensional/1'>Residue 1000</scene>
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</script>
+
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<text>400</text>
+
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<checked>false</checked>
+
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</item>
+
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<item>
+
-
<script>{*.ca}.property_t = [20, 18, 17, 18, 16, 17, 19, 18, 17, 18, 18, 17, 17, 18, 18, 20, 18, 19, 17, 18, 18, 20, 20, 20, 21, 20, 19, 21, 20, 20, 20, 19, 20, 20, 20, 20, 21, 20, 21, 21, 21, 19, 20, 20, 18, 20, 20, 20, 18, 18, 19, 18, 20, 18, 19, 19, 19, 19, 21, 21, 19, 19, 21, 20, 19, 20, 19, 20, 20, 20, 19, 19, 19, 21, 18, 19, 18, 18, 18, 17, 18, 19, 18, 17, 17, 17, 18, 18, 17, 18, 18, 17, 19, 18, 17, 19, 17, 18, 18, 18, 18, 18, 18, 19, 18, 19, 19, 20, 19, 19, 20, 20, 20, 20, 21, 19, 20, 22, 21, 20, 21, 22, 20, 20, 21, 19, 20, 18, 20, 17, 17, 18, 15, 16, 16, 16, 17, 15, 13, 11, 10, 12, 12, 14, 15, 17, 16, 13, 12, 11, 13, 14, 14, 15, 13, 13, 13, 15, 15, 14, 14, 16, 15, 15, 17, 17, 18, 17, 18, 17, 19, 17, 18, 16, 18, 18, 16, 15, 15, 15, 16, 16, 14, 13, 11, 10, 10, 13, 13, 11, 13, 14, 14, 13, 15, 16, 14, 14, 16, 16, 14, 17, 17, 15, 18, 16, 17, 16, 15, 16, 14, 14, 13, 15, 13, 15, 15, 16, 13, 12, 12, 12, 12, 10, 11, 9, 10, 13, 11, 9, 10, 10, 10, 9, 12, 11, 11, 13, 12, 14, 15, 15, 15, 15, 13, 15, 14, 17, 15, 17, 17, 18, 16, 17, 17, 14, 13, 15, 14, 12, 13, 15, 13, 11, 13, 12, 15, 15, 16, 14, 17, 16, 18, 19, 19, 18, 18, 19, 19, 21, 20, 19, 18, 19, 20, 20, 18, 18, 19, 20, 19, 18, 19, 20, 18, 17, 19, 18, 17, 17, 18, 17, 17, 16, 16, 17, 18, 17, 18, 16, 17, 19, 20, 20, 20, 19, 20, 21, 20, 20, 19, 20, 19, 21, 18, 17, 18, 18, 18, 19, 19, 16, 15, 16, 13, 13, 12, 11, 11, 9, 10, 7, 8, 8, 9, 9, 9, 8, 9, 8, 10, 10, 9, 8, 7, 6, 6, 4, 4, 3, 4, 5, 5, 6, 8, 7, 7, 7, 8, 8, 7, 8, 11, 10, 10, 10, 10, 10, 9, 9, 8, 10, 8, 8, 8, 6, 6, 6, 7, 5, 6, 6, 6, 4, 4, 6, 6, 5, 5, 6, 6, 9, 8, 9, 11, 12, 11, 11, 10, 11, 12, 10, 10, 11, 11, 8, 7, 10, 9, 8, 9, 10, 10, 9, 7, 7, 8, 8, 7, 9, 7, 6, 6, 5, 9, 10, 10, 11, 10, 10, 9, 11, 11, 10, 9, 11, 9, 7, 8, 9, 9, 7, 7, 8, 5, 9, 10, 10, 11, 12, 11, 13, 13, 13, 13, 12, 13, 12, 12, 11, 13, 11, 11, 12, 11, 11, 10, 9, 9, 9, 6, 10, 9, 11, 11, 11, 13, 12, 12, 11, 11, 11, 12, 12, 12, 13, 10, 12, 12, 12, 11, 12, 13, 12, 13, 12, 13, 12, 15, 14, 13, 13, 13, 12, 12, 11, 11, 9, 9, 7, 8, 5, 8, 9, 6, 9, 8, 9, 9, 10, 12, 11, 12, 12, 12, 11, 12, 10, 8, 10, 11, 8, 9, 11, 10, 8, 11, 11, 11, 11, 12, 12, 11, 11, 12, 9, 8, 7, 6, 5, 5, 5, 6, 6, 6, 7, 8, 8, 8, 8, 8, 7, 8, 6, 7, 8, 4, 5, 6, 6, 5, 6, 6, 6, 6, 8, 7, 6, 7, 9, 7, 7, 7, 5, 5, 4, 3, 2, 1, 0, 1, 3, 4, 4, 7, 7, 6, 5, 6, 8, 10, 7, 6, 10, 8, 6, 9, 11, 8, 8, 10, 12, 13, 13, 10, 11, 11, 11, 11, 11, 9, 9, 10, 7, 8, 9, 8, 7, 8, 10, 12, 15, 14, 17, 18, 19, 19, 19, 21, 21, 21, 23, 23, 23, 26, 25, 23, 25, 27, 26, 22, 25, 25, 23, 22, 23, 23, 21, 21, 21, 22, 23, 24, 25, 25, 27, 27, 25, 27, 26, 27, 26, 29, 28, 27, 28, 29, 29, 29, 29, 27, 28, 27, 26, 27, 25, 26, 26, 23, 24, 26, 24, 24, 24, 24, 23, 23, 23, 22, 20, 22, 20, 23, 23, 24, 23, 22, 23, 21, 22, 23, 24, 24, 23, 27, 26, 25, 26, 27, 27, 27, 28, 28, 28, 29, 29, 29, 29, 29, 30, 30, 29, 29, 29, 29, 28, 29, 29, 28, 29, 27, 28, 28, 28, 28, 29, 29, 29, 28, 27, 27, 27, 26, 26, 26, 26, 26, 26, 25, 27, 27, 25, 26, 28, 27, 28, 27, 29, 27, 28, 29, 28, 30, 29, 28, 29, 29, 29, 28, 29, 30, 29, 28, 30, 30, 29, 30, 29, 29, 29, 28, 27, 28, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 28, 28, 29, 29, 29, 29, 30, 29, 29, 29, 30, 29, 28, 28, 27, 28, 27, 28, 27, 28, 28, 26, 28, 27, 27, 27, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 28, 28, 27, 27, 27, 25, 26, 26, 25, 25, 27, 26, 26, 27, 27, 27, 28, 28, 29, 28, 29, 28, 28, 29, 29, 28, 28, 29, 29, 28, 27, 29, 29, 27, 28, 28, 28, 26, 28, 29, 27, 28, 28, 29, 28, 29, 27, 28, 28, 29, 29, 29, 29, 29, 30, 29, 28, 30, 29, 29, 29, 28, 29, 29, 29, 30, 30, 30, 29, 30, 29, 29, 30, 29, 30, 30, 30, 30, 30, 30, 30, 29, 30, 29, 29, 28, 29, 29, 29, 27, 28, 28, 26, 26, 26, 25, 26, 25, 26, 26, 26, 26, 24, 25, 26, 27, 27, 26, 26, 27, 26, 26, 25, 22, 22, 19, 22, 24, 24, 24, 24, 26, 25, 25, 26, 26, 25, 26, 26, 27, 27, 26, 28, 28, 28, 28, 29, 29, 29, 29, 28, 29, 28, 30, 29, 29, 29, 29, 29, 30, 30, 29, 29, 29, 30, 29, 27, 29, 29, 30, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 28, 29, 28, 28, 29, 27, 29, 27, 28, 27, 28, 29, 26, 28, 28, 26, 29, 28, 29, 28, 28, 29, 30, 30, 30, 30, 29, 30, 29, 30, 30, 30, 29, 29, 29, 28, 29, 28, 29, 28, 29, 29, 29, 27, 28, 29, 28, 27, 28, 29, 27, 27, 29, 29, 28, 27, 25, 25, 27, 27, 25, 26, 27, 26, 24, 26, 27, 25, 26, 27, 27, 26, 28, 27, 27, 26, 28, 28, 28, 28, 30, 29, 29, 29, 30, 30, 30, 30, 30, 29, 30, 30, 28, 29, 29, 28, 27, 28, 28, 28, 27, 27, 26, 27, 28, 29, 29, 27, 28, 27, 27, 28, 27, 28, 26, 27, 28, 27, 28, 26, 29, 28, 28, 29, 29, 28, 29, 30, 30, 29, 29, 29, 30, 30, 29, 29, 29, 29, 29, 29, 29, 29, 27, 28, 28, 28, 28, 28, 26, 27, 28, 26, 28, 28, 29, 28, 29, 29, 29, 28, 27, 28, 25, 27, 27, 25, 28, 25, 28, 29, 29, 30, 30, 29, 29, 30, 29, 29, 30, 30, 30, 29, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29, 28, 28, 26, 27, 29, 28, 30, 29, 29, 30];
+
-
select alpha; color property_t; spacefill off; label off;
+
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set hoverlabel "residue %r vs 600: %[property_t] Å";
+
-
select 600 and alpha; spacefill on; color yellow;
+
-
</script>
+
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<text>600</text>
+
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<checked>false</checked>
+
-
</item>
+
-
<item>
+
-
<script>{*.ca}.property_t = [29, 30, 29, 30, 29, 30, 30, 29, 30, 30, 29, 29, 30, 30, 29, 29, 29, 29, 28, 28, 29, 28, 29, 28, 28, 29, 29, 28, 29, 30, 29, 30, 29, 29, 29, 30, 29, 30, 30, 30, 30, 30, 30, 29, 30, 29, 28, 27, 29, 28, 27, 28, 28, 29, 30, 30, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 30, 30, 29, 30, 30, 29, 29, 29, 29, 29, 29, 28, 29, 29, 28, 28, 28, 29, 28, 30, 28, 28, 29, 28, 27, 28, 28, 30, 29, 30, 30, 29, 30, 30, 30, 29, 30, 30, 29, 29, 30, 30, 29, 30, 30, 30, 30, 30, 30, 30, 30, 29, 30, 29, 30, 30, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 26, 28, 27, 27, 27, 27, 25, 26, 27, 28, 29, 27, 28, 28, 27, 28, 28, 28, 28, 29, 28, 28, 29, 29, 29, 29, 29, 29, 29, 30, 30, 29, 29, 30, 30, 29, 30, 30, 30, 29, 29, 29, 29, 28, 28, 27, 27, 25, 25, 26, 26, 25, 27, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 30, 30, 29, 30, 30, 30, 29, 30, 30, 30, 29, 28, 28, 27, 27, 26, 26, 24, 26, 26, 23, 24, 24, 22, 24, 27, 26, 24, 24, 22, 25, 27, 26, 26, 28, 27, 27, 28, 29, 28, 27, 28, 28, 29, 29, 28, 28, 25, 26, 25, 25, 23, 27, 26, 22, 23, 25, 24, 22, 24, 26, 24, 23, 27, 28, 26, 28, 28, 30, 29, 29, 27, 28, 27, 27, 27, 25, 27, 27, 24, 26, 25, 25, 26, 26, 26, 27, 27, 26, 28, 29, 28, 26, 27, 28, 27, 26, 27, 29, 26, 28, 29, 29, 26, 29, 27, 29, 29, 29, 28, 28, 28, 25, 26, 28, 27, 28, 29, 29, 28, 28, 29, 29, 28, 29, 29, 29, 29, 29, 29, 29, 29, 30, 29, 30, 29, 29, 29, 28, 29, 30, 29, 28, 28, 27, 26, 25, 24, 23, 26, 25, 26, 28, 28, 29, 27, 26, 26, 29, 26, 26, 27, 27, 28, 27, 27, 27, 29, 28, 29, 28, 29, 28, 28, 28, 29, 28, 28, 29, 29, 28, 28, 27, 25, 28, 27, 26, 27, 26, 26, 24, 26, 26, 25, 24, 25, 26, 26, 24, 26, 26, 26, 27, 28, 29, 28, 29, 28, 28, 29, 28, 30, 29, 29, 29, 28, 28, 28, 27, 27, 27, 27, 26, 24, 26, 26, 24, 24, 25, 25, 22, 25, 26, 26, 27, 27, 28, 29, 29, 29, 30, 30, 29, 29, 29, 29, 28, 28, 28, 27, 26, 26, 27, 26, 27, 27, 28, 27, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29, 28, 28, 27, 28, 28, 29, 28, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 30, 30, 30, 29, 30, 30, 30, 29, 30, 30, 29, 30, 30, 30, 29, 29, 29, 29, 30, 29, 28, 29, 28, 30, 28, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 30, 30, 29, 30, 30, 29, 30, 29, 30, 29, 30, 30, 29, 29, 30, 30, 29, 30, 29, 29, 28, 29, 28, 29, 28, 28, 28, 29, 30, 28, 29, 29, 30, 29, 29, 28, 27, 27, 29, 27, 26, 28, 29, 26, 26, 29, 29, 27, 27, 30, 28, 27, 29, 29, 29, 29, 28, 27, 28, 27, 28, 26, 25, 25, 27, 26, 27, 23, 27, 26, 25, 27, 28, 27, 29, 28, 28, 28, 29, 28, 29, 29, 29, 29, 30, 29, 30, 30, 29, 29, 30, 29, 29, 30, 29, 29, 29, 29, 28, 28, 28, 28, 28, 27, 26, 25, 23, 24, 22, 20, 18, 18, 18, 17, 16, 16, 15, 17, 14, 14, 15, 14, 13, 12, 14, 12, 11, 10, 11, 11, 9, 9, 10, 12, 11, 12, 13, 13, 13, 12, 13, 12, 13, 13, 14, 14, 12, 12, 13, 12, 13, 11, 12, 10, 11, 12, 10, 9, 12, 10, 9, 10, 9, 10, 9, 9, 9, 9, 10, 10, 9, 10, 12, 10, 10, 11, 10, 8, 9, 8, 8, 8, 7, 8, 8, 8, 8, 9, 7, 8, 9, 9, 10, 9, 10, 10, 11, 11, 12, 10, 11, 12, 11, 11, 7, 5, 4, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 0, 1, 1, 1, 2, 2, 3, 3, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 3, 3, 3, 3, 4, 3, 3, 3, 4, 4, 3, 5, 5, 4, 5, 6, 7, 7, 8, 8, 9, 8, 9, 10, 9, 10, 11, 11, 11, 10, 11, 10, 10, 10, 10, 11, 11, 13, 13, 12, 11, 12, 11, 11, 11, 10, 10, 11, 11, 9, 9, 9, 9, 8, 8, 8, 8, 9, 9, 9, 8, 9, 9, 8, 8, 8, 9, 8, 7, 8, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 9, 8, 9, 8, 9, 10, 8, 9, 9, 9, 9, 10, 10, 8, 9, 8, 8, 8, 8, 8, 8, 8, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 8, 9, 10, 10, 10, 10, 11, 12, 12, 11, 12, 10, 11, 10, 8, 9, 8, 8, 8, 8, 8, 9, 9, 9, 9, 10, 10, 11, 10, 10, 10, 9, 9, 9, 10, 10, 10, 11, 11, 11, 12, 12, 12, 12, 12, 11, 10, 9, 9, 9, 8, 8, 8, 7, 7, 8, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 8, 7, 7, 7, 7, 7, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 8, 7, 7, 8, 8, 8, 8, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 10, 11, 11, 11, 11, 11, 11, 10, 11, 11, 10, 10, 9, 9, 9, 10, 10, 10, 10, 10, 9, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 8, 7, 8, 8, 8, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 5, 6, 5, 6, 6, 7, 5, 6, 7, 7, 7, 7, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 9, 9, 9, 8, 8, 7, 7, 8, 8, 9, 9, 9, 8, 10, 9, 8, 10, 9, 10, 9, 9, 10, 9, 9, 8, 8, 7, 7, 6, 6, 6, 7, 7, 8, 8, 9, 8, 8, 9, 9]
+
-
select alpha; color property_t; spacefill off; label off;
+
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set hoverlabel "residue %r vs 800: %[property_t] Å";
+
-
select 800 and alpha; spacefill on; color yellow;
+
-
</script>
+
-
<text>800</text>
+
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<checked>false</checked>
+
-
</item>
+
-
<item>
+
-
<script>{*.ca}.property_t = [28, 28, 28, 28, 28, 28, 28, 29, 29, 28, 29, 29, 29, 29, 28, 28, 28, 29, 28, 28, 28, 28, 30, 28, 27, 29, 30, 27, 29, 29, 29, 29, 30, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 29, 30, 29, 29, 30, 28, 27, 29, 29, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 30, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 29, 29, 28, 29, 28, 29, 29, 29, 27, 28, 29, 29, 29, 29, 29, 29, 29, 27, 29, 29, 29, 30, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 29, 29, 29, 28, 29, 29, 28, 28, 28, 28, 28, 29, 29, 28, 28, 28, 28, 28, 26, 28, 27, 27, 27, 27, 26, 26, 27, 27, 27, 25, 27, 27, 27, 28, 27, 27, 28, 28, 29, 28, 29, 29, 27, 29, 29, 29, 28, 29, 29, 29, 29, 29, 28, 29, 29, 28, 28, 27, 29, 28, 28, 28, 28, 27, 28, 27, 25, 26, 26, 25, 25, 27, 26, 26, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 28, 28, 26, 27, 25, 26, 24, 26, 25, 25, 26, 25, 25, 25, 25, 25, 25, 25, 27, 25, 26, 26, 25, 26, 27, 26, 26, 28, 28, 28, 27, 28, 28, 28, 26, 26, 27, 26, 25, 25, 24, 26, 25, 26, 26, 24, 25, 26, 23, 25, 27, 26, 26, 28, 27, 27, 28, 28, 29, 28, 27, 27, 26, 27, 27, 26, 27, 26, 25, 25, 27, 26, 27, 26, 26, 27, 26, 26, 28, 29, 29, 26, 27, 28, 28, 26, 27, 28, 27, 27, 28, 29, 27, 28, 27, 28, 29, 28, 27, 28, 28, 26, 26, 28, 29, 29, 30, 29, 28, 29, 29, 28, 28, 29, 29, 28, 29, 29, 29, 29, 29, 29, 28, 29, 29, 28, 28, 28, 28, 28, 28, 28, 27, 26, 25, 25, 25, 26, 25, 26, 27, 28, 29, 28, 27, 27, 28, 28, 27, 26, 28, 27, 28, 27, 28, 28, 29, 28, 28, 28, 29, 28, 28, 28, 29, 27, 28, 29, 29, 28, 27, 27, 26, 26, 26, 25, 25, 26, 24, 26, 26, 26, 24, 25, 26, 26, 26, 25, 26, 27, 28, 27, 28, 28, 29, 29, 28, 28, 29, 29, 29, 29, 28, 28, 28, 28, 28, 27, 26, 26, 26, 26, 23, 25, 26, 24, 25, 25, 23, 26, 24, 26, 27, 28, 27, 28, 29, 29, 29, 29, 29, 29, 29, 29, 27, 27, 28, 28, 26, 26, 26, 26, 26, 28, 27, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 29, 29, 28, 28, 28, 28, 28, 28, 26, 28, 27, 28, 28, 28, 30, 29, 30, 29, 29, 28, 29, 30, 29, 29, 29, 28, 28, 29, 29, 28, 28, 29, 29, 28, 28, 29, 29, 28, 28, 29, 28, 28, 28, 28, 27, 29, 28, 28, 28, 27, 29, 29, 29, 29, 29, 29, 29, 29, 30, 29, 29, 29, 29, 28, 28, 29, 29, 29, 29, 29, 29, 29, 28, 29, 29, 28, 28, 29, 29, 28, 29, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 28, 29, 28, 29, 29, 29, 29, 28, 29, 29, 29, 29, 28, 27, 27, 28, 28, 27, 28, 29, 28, 27, 29, 29, 27, 28, 29, 28, 27, 27, 28, 27, 28, 28, 27, 28, 29, 28, 28, 26, 26, 28, 26, 27, 26, 28, 28, 27, 28, 27, 28, 28, 28, 28, 28, 28, 29, 29, 28, 29, 29, 29, 28, 29, 28, 28, 28, 28, 29, 28, 28, 29, 29, 28, 28, 29, 28, 28, 27, 28, 27, 26, 25, 22, 24, 23, 21, 19, 20, 20, 18, 18, 16, 16, 16, 16, 15, 15, 14, 15, 15, 15, 14, 14, 14, 14, 13, 12, 13, 13, 15, 12, 14, 13, 13, 14, 13, 13, 14, 15, 14, 15, 16, 15, 16, 16, 17, 16, 16, 16, 15, 15, 16, 15, 16, 16, 15, 14, 14, 14, 14, 14, 13, 13, 13, 13, 13, 12, 13, 13, 12, 11, 11, 12, 10, 9, 10, 10, 10, 12, 10, 10, 10, 11, 12, 11, 10, 11, 12, 12, 13, 12, 14, 14, 14, 15, 16, 15, 15, 15, 15, 15, 12, 11, 10, 9, 9, 9, 8, 8, 7, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 8, 6, 5, 7, 7, 7, 7, 8, 7, 7, 8, 8, 8, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 8, 7, 8, 8, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 7, 7, 7, 6, 5, 6, 6, 6, 5, 5, 5, 5, 6, 6, 6, 6, 8, 7, 7, 8, 8, 8, 9, 9, 9, 8, 9, 9, 8, 7, 7, 7, 6, 6, 7, 6, 5, 6, 6, 7, 7, 6, 6, 7, 6, 6, 7, 7, 8, 7, 8, 9, 9, 8, 7, 7, 7, 7, 6, 6, 7, 7, 8, 7, 8, 9, 9, 8, 8, 8, 8, 9, 9, 10, 10, 10, 9, 10, 9, 9, 9, 9, 8, 8, 8, 8, 8, 7, 8, 8, 8, 7, 8, 8, 6, 7, 7, 7, 6, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 3, 3, 3, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 3, 3, 3, 3, 3, 4, 4, 3, 4, 5, 4, 5, 5, 4, 4, 4, 5, 5, 4, 5, 6, 6, 6, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 3, 3, 3, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 4, 5, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 3, 3, 3, 3, 2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 3, 2, 2, 2, 1, 1, 1, 1, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 4, 4, 3, 3, 4, 3, 3, 3, 3, 3, 4, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 4, 5, 4, 5, 5, 5];
+
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select alpha; color property_t; spacefill off; label off;
+
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set hoverlabel "residue %r vs 1000: %[property_t] Å";
+
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select 1000 and alpha; spacefill on; color yellow;
+
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</script>
+
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<text>1000</text>
+
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<checked>true</checked>
+
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</item>
+
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</jmolRadioGroup>
+
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</jmol>
+
[[Image:Position_error_alphafold_P13009.jpg|350px]]
[[Image:Position_error_alphafold_P13009.jpg|350px]]

Revision as of 14:50, 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

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/AlphaFold_pLDDT_and_expected_distance_error"
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