AlphaFold2 examples from CASP 14: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 18: | Line 18: | ||
===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. 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. <scene name='87/875686/Dali_5a2f_vs_7jx6_yale/1'>The structural similarity between Dali's top hit and 7jx6</scene> is not as close as for AlphaFold2's prediction, but is closer than the 2nd best prediction (see Table I below). Dali's top hit has a single disulfide bond (compare with Table I). 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>. | 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 the 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. <scene name='87/875686/Dali_5a2f_vs_7jx6_yale/1'>The structural similarity between Dali's top hit and 7jx6</scene><ref name="yale">Structural alignment by Dali. Interpolation by the [http://www2.molmovdb.org/wiki/info/index.php/Morph2_Server Yale Morph2 Server]. Homogenization method: homology modeling. No minimization. This produced a 9-model file where model 1 was 7jx6, and models 2-9 were interpolations. 5a2f residues 28-133 were added as model 10 (black in the molecular scene).</ref> is not as close as for AlphaFold2's prediction, but is closer than the 2nd best prediction (see Table I below). Dali's top hit has a single disulfide bond (compare with Table I). 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=== | ||
