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/Chain_a_of_7jx6/1'>Here is one chain of ORF8</scene> from the higher resolution X-ray structure, [[7jx6]]. These chains form [http://firstglance.jmol.org/fg.htm?mol=7jx6 disulfide-linked dimers], and the dimers form higher order multimers<ref name="multimers">PMID: 33361333</ref> (not shown). | <scene name='87/875686/Chain_a_of_7jx6/1'>Here is one chain of ORF8</scene> from the higher resolution X-ray structure, [[7jx6]]. These chains form [http://firstglance.jmol.org/fg.htm?mol=7jx6 disulfide-linked dimers], and the dimers form higher order multimers<ref name="multimers">PMID: 33361333</ref> (not shown). Notice that the <span class="text-blue"><b>amino</b></span> and <span class="text-red"><b>carboxy</b></span> ends of the chain come together to form an anti-parallel beta sheet. Also notice that there are 3 disulfide bonds. An accurate prediction would include both of these features. | ||
<scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene><ref name="imf">Alignment by Swiss-PdbViewer's ''iterative magic fit''. This starts with a sequence alignment-guided structural alignment, and then selects subsets of the structures to minimize the RMSD. Eight intermediate structures were generated by the [[Morphs#Linear_Morph_Server|Theis Morph Server]] by linear interpolation.</ref>. The only substantial disagreement is for a large surface loop, sequence range 48-57. See the TABLE below for [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD] values. | <scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene><ref name="imf">Alignment by Swiss-PdbViewer's ''iterative magic fit''. This starts with a sequence alignment-guided structural alignment, and then selects subsets of the structures to minimize the RMSD. Eight intermediate structures were generated by the [[Morphs#Linear_Morph_Server|Theis Morph Server]] by linear interpolation.</ref>. The only substantial disagreement is for a large surface loop, sequence range 48-57. See the TABLE below for [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD] values. | ||
