AlphaFold pLDDT and expected distance error: Difference between revisions

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Karsten Theis (talk | contribs)
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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>
  <jmolRadioGroup>
 
    <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;
<scene name='92/920232/Two_dimensional_800/1'>Residue 800</scene>
set hoverlabel "residue %r vs 400: %[property_t] \u00c5";
 
select 400 and alpha; spacefill on; color yellow;
<scene name='92/920232/Two_dimensional/1'>Residue 1000</scene>
</script>
      <text>400</text>
      <checked>false</checked>
    </item>
    <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;
set hoverlabel "residue %r vs 600: %[property_t] Å";
select 600 and alpha; spacefill on; color yellow;
</script>
      <text>600</text>
      <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;
set hoverlabel "residue %r vs 800: %[property_t] Å";
select 800 and alpha; spacefill on; color yellow;
</script>
      <text>800</text>
      <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];
select alpha; color property_t; spacefill off; label off;
set hoverlabel "residue %r vs 1000: %[property_t] Å";
select 1000 and alpha; spacefill on; color yellow;
</script>
      <text>1000</text>
      <checked>true</checked>
    </item>
  </jmolRadioGroup>
</jmol>


[[Image:Position_error_alphafold_P13009.jpg|350px]]
[[Image:Position_error_alphafold_P13009.jpg|350px]]

Revision as of 17:50, 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.

pLDDT

The pLDDT value is assigned to each individual residue and stored in coordinate files instead of temperature factors. Different from temperature factors, high values indicate high confidence in atomic positions, and low values low confidence. This value is named pLDDT because it predicts the so-called LDDT value (Local Distance Difference Test, [1]), a way to characterize the difference of two related conformations without aligning the structures.

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 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.

Residues on the apparent domain interface

Drag the structure with the mouse to rotate
  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?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Eric Martz
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