AlphaFold2 examples from CASP 14: Difference between revisions

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The quality of predictions for the structure of ORF8 are judged by comparison with X-ray crystallographic [[empirical models]] which were not available to the groups making predictions. Shortly after the CASP 14 competition (summer 2020), two X-ray crystal structures were reported for ORF8: [[7jtl]] released August 26, 2020, and [[7jx6]], released September 23, 2020. The [[resolution|resolutions]] are 2.0 and 1.6 Å respectively, and both have worse than average [[Rfree]] values.
The quality of predictions for the structure of ORF8 are judged by comparison with X-ray crystallographic [[empirical models]] which were not available to the groups making predictions. Shortly after the CASP 14 competition (summer 2020), two X-ray crystal structures were reported for ORF8: [[7jtl]] released August 26, 2020, and [[7jx6]], released September 23, 2020. The [[resolution|resolutions]] are 2.0 and 1.6 Å respectively, and both have worse than average [[Rfree]] values.
{{Template:Green links zoom}}
{{Template:Green links zoom}}
<scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene>: 87 of the 102 residues/chain (85%) align with a [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions root mean square deviation] '''(RMSD) of 0.66 Å'''<ref name="imf">Alignment and RMSD calculation was by ''iterative magic fit'' of Swiss PDB Viewer.</ref>. When sidechains are included, 829 atoms (90% of 918 total) aligned with RMSD 4.3 Å<ref name="mf">Alignment and RMSD calculation was by ''magic fit'' of Swiss PDB Fiewer.</ref>, and 348 atoms (38%) aligned with RMSD 0.71 Å<ref name="imf" />.
<scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene>. See TABLE below for [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD] values.


===AlphaFold2 Prediction for ORF8===
===AlphaFold2 Prediction for ORF8===
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|+ ORF8 Alignments With Chain A of [[7jx6]]
|+ ORF8 Alignments With Chain A of [[7jx6]]
|-
|-
! Model || GDT_TS || C&alpha; RMSD, Å || C&alpha; Aligned || RMSD Including<br>Sidechains, Å || Atoms Aligned
! Model || GDT_TS || C&alpha; [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD], Å || C&alpha; Aligned || [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD] Including<br>Sidechains, Å || Atoms Aligned
|-
|-
| [[7jtl]]:A ||  ||  4.02<br>'''0.66''' || 102/102 (100%)<br>'''87/102 (85%)''' || 4.3<br>'''1.58''' || 829/829 (100%)<br>'''709/829 (86%)'''
| [[7jtl]]:A ||  ||  4.02<br>'''0.66''' || 102/102 (100%)<br>'''87/102 (85%)''' || 4.3<br>'''1.58''' || 829/829 (100%)<br>'''709/829 (86%)'''
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