AlphaFold pLDDT and expected distance error

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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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AlphaFold provides two measures of coordinate error. The residue-by-residue pLDDT value are stored directly in the coordinate file, and the pairwise residue distance error stored in a separate file. Here, we use the bacterial methionine synthase as [https://alphafold.ebi.ac.uk/entry/A0A485DTP7 an example for a predicted structure].
<StructureSection load='' size='350' side='right' caption='' scene='92/920232/One_dimensional/1'>
<StructureSection load='' size='350' side='right' caption='' scene='92/920232/One_dimensional/1'>
==pLDDT==
==pLDDT==
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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, <ref>PMID: 23986568</ref>), a way to characterize the difference of two related conformations without aligning the structures.
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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 (scale of 0 to 100). This value is named pLDDT because it predicts the so-called LDDT value (Local Distance Difference Test, <ref>PMID: 23986568</ref>), a way to characterize the difference of two related conformations without aligning the structures.
==Expected distance error==
==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. 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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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]], e.g. for the cap subdomain (click on 680 below) that plays a role in protecting B12 from unwanted redox reactions.
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Residue <jmol>
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<jmolLink>
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<script> script "/wiki/images/d/d4/Res200.spt"</script>
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<item>
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<text>Residue 200</text>
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<script>script "/wiki/images/d/d4/Res200.spt"</script>
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</jmolLink>
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<text>200</text>
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<script>script "/wiki/images/2/28/Res280.spt"</script>
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<text>280</text>
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<checked>false</checked>
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<item>
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<script>script "/wiki/images/1/1c/Res400.spt"</script>
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<text>400</text>
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<checked>false</checked>
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<script>script "/wiki/images/7/79/Res600.spt"</script>
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<text>600</text>
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<checked>false</checked>
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<item>
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<script>script "/wiki/images/6/6d/Res680.spt"</script>
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<text>680</text>
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<checked>false</checked>
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</item>
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<item>
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<script>script "/wiki/images/c/c8/Res800.spt"</script>
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<text>800</text>
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<checked>false</checked>
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<item>
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<script>script "/wiki/images/7/72/Res1000.spt"</script>
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<text>1000</text>
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<checked>true</checked>
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<jmol>
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</jmolRadioGroup>
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<jmolLink>
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<script> script "/wiki/images/2/28/Res280.spt"</script>
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<text>Residue 280</text>
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</jmolLink>
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</jmol>
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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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<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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<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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<jmol>
 
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<jmolLink>
 
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<script> script "/wiki/images/c/c8/Res800.spt"</script>
 
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<text>Residue 800</text>
 
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</jmolLink>
 
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</jmol>
 
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<jmol>
 
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<jmolLink>
 
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<script> script "/wiki/images/7/72/Res1000.spt"</script>
 
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<text>Residue 1000</text>
 
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</jmolLink>
 
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</jmol>
 

Revision as of 16:21, 18 August 2022

AlphaFold provides two measures of coordinate error. The residue-by-residue pLDDT value are stored directly in the coordinate file, and the pairwise residue distance error stored in a separate file. Here, we use the bacterial methionine synthase as an example for a predicted structure.

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?)

Karsten Theis, Eric Martz

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