AlphaFold2 examples from CASP 14: Difference between revisions
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===ORF8 is not a novel fold=== | ===ORF8 is not a novel fold=== | ||
Less than 2% of new [[empirically-determined structures]] have novel folds; that is, folds not aready represented in the [[PDB]]<ref name="cath2011">PMID: 21097779</ref>. When chain A of [[7jx6]] was submitted to Dali<ref name="dali2020">PMID: 31606894</ref> (February, 2021), the top hit was the N-terminal domain of two domains in [[5a2f]], the CD166 human cell surface receptor involved in activation of T lymphocytes. The Z-score was 7.1, and 88 alpha carbons aligned with RMSD 3.2 Å. Dali reported the identity as 6% in | Less than 2% of new [[empirically-determined structures]] have novel folds; that is, folds not aready represented in the [[PDB]]<ref name="cath2011">PMID: 21097779</ref>. When chain A of [[7jx6]] was submitted to Dali<ref name="dali2020">PMID: 31606894</ref> (February, 2021), the top hit was the N-terminal domain of two domains in [[5a2f]], the CD166 human cell surface receptor involved in activation of T lymphocytes. The Z-score was 7.1, and 88 alpha carbons aligned with RMSD 3.2 Å. Swiss-PdbViewer obtained RMSD 1.95 Å for 48 alpha carbons<ref name="fitselimprov">Using Swiss-PdbViewer's ''Fit from Selection'' with 102 residues selected from each structure, followed by ''Improve Fit''.</ref>. Dali reported the identity as 6% in its structure-based sequence alignment. Sequence alignment by MAFFT<ref name="mafft">PMID: 23329690</ref> obtained 18% sequence identity using more and larger gaps. The structural similarity between Dali's top hit and 7jx6 is not as close as for AlphaFold2's prediction, but is closer than the 2nd best prediction (see Table I below). In conclusion, '''ORF8 does not have a novel fold'''<ref name="holm">The interpretation of Dali's result to mean that ORF8 does not have a novel fold was kindly confirmed by Liisa Holm, personal communication to [[User:Eric Martz|Eric Martz]].</ref>. | ||
===AlphaFold2 Prediction for ORF8=== | ===AlphaFold2 Prediction for ORF8=== | ||
