AlphaFold2 examples from CASP 14: Difference between revisions

<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 I below for [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions RMSD] values.

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/2'>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>.

|+ Table I. ORF8 Predictions Aligned With Chain A of [[7jx6]]

! Model || GDT_TS || Disulfde<br>Bonds || 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

:Alignments by "Magic Fit"<ref name="mf">Alignment by Swiss-PdbViewer's ''magic fit''. This is a sequence alignment-guided structural alignment. Eight intermediate structures were generated by the [[Morphs#Linear_Morph_Server|Theis Morph Server]] by linear interpolation.</ref> of Swiss-PdbViewer 4.1.<br>

:'''Alignments by "Iterative Magic Fit"<ref name="imf" /> of Swiss-PdbViewer 4.1.'''<br>

:† Iterative Magic Fit was unable to align.<br>

The third best prediction for ORF8 was by the Perez Lab, with GDT_TS 33 (see Table I above). It '''correctly predicted the parallel beta strands formed by the amino and carboxy terminal ends of the chain'''. <scene name='87/875686/3rd_best_orf8/1'>When the 2-stranded parallel beta strands formed by the ends of the chains are aligned, the remainder aligns poorly</scene>. This prediction has '''no disulfide bonds'''. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with two incorrectly predicted salt bridges.

Among predictions by automated servers for all ~100 CASP 14 targets, the top ranking server was QUARK from the Yang Zhang group (Univ. Michigan). For ORF8, the Zhang-TBM server made the best server prediction with a '''GDT_TS of 27'''. (The prediction by QUARK was almost as good, GDT_TS 26.) The prediction has the '''two chain termini not parallel, and the amino terminus is not a beta strand''', differing in both respects from the X-ray model. Also, '''no disulfide bonds''' are predicted. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with several incorrectly predicted salt bridges. The structural alignment is very poor and is not shown.

Among predictions for all ~100 CASP 14 targets, the group of David Baker [https://predictioncenter.org/casp14/zscores_final.cgi ranked second]. The Rosetta Server of the Baker group ranked 18th overall, but was the 4th ranked server<ref name="serverranks">For all targets in CASP 14, the top two servers were QUARK and Zhang-server (which were not significantly different at a Z-score sum of 62.9), followed by Zhang-CEthreader (55.9) and BAKER-ROSETTASERVER (55.3).</ref>. [https://predictioncenter.org/casp14/results.cgi?view=tables&target=T1064-D1&model=1&groups_id= For ORF8, the Rosetta Server prediction GDT_TS was 26], a bit better than the median of 23. The Rosetta Server's prediction for ORF8 has '''the two termini far apart''' (C&alpha; 13 Å or farther apart), a substantial difference from the X-ray structure (C&alpha; mostly ~5 Å apart). It predicts '''two disulfide bonds, but neither matches''' the pairs of Cys residues in the actual disulfide bonds.  The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with one incorrectly predicted salt bridge. The structural alignment is very poor and is not shown.