This issue collects and reports on the status of issues which we know (and are in the process of fixing) about our display of SARS-CoV-2 proteins and user-annotations:
[x] Heteromer models (which we can create with SWISS-MODEL and list on our SARS-CoV-2 page) are not yet visible for use with annotations. This requires some larger changes but we are working on it.
[x] In the display for the polyprotein some structures are not properly mapped to the "Uridylate-specific endoribonuclease" and "2'-O-methyltransferase" parts (i.e. clicking on them doesn't show all structures for that part but the structures are available in the table at the bottom of the page). We will fix that...
[x] Some PDB structures are linked to P0DTC1 instead of P0DTD1. This is a rather random choice (P0DTC1 is mainly a subset of P0DTD1 as described e.g. here) and we are improving how we deal with that (together with PDBe-SIFTS team). Generally we prefer to ignore P0DTC1 and use P0DTD1 only.
[ ] Make sure that we can nicely display annotations on different subunits of heteromers if they have different UniProt-sequences (e.g. in example mentioned here, you should be able to see ACE2 and spike annotations at the same time on a suitable heteromer).
[ ] Include models from custom modeling efforts (we could include extra models from our own efforts that go beyond SWISS-MODEL's built-in capabilities)
[ ] Expand coverage with selected models from other predictors (specifically Feig+AlphaFold, CASP community, Robetta, C-I-TASSER). We focus on cases where we expect that models are high-quality enough to be of use for analyzing structure-mapped annotations.
Please add comments here if you find new issues and I will update the list accordingly and coordinate the work in the SWISS-MODEL team to fix those issues.
This issue collects and reports on the status of issues which we know (and are in the process of fixing) about our display of SARS-CoV-2 proteins and user-annotations:
Please add comments here if you find new issues and I will update the list accordingly and coordinate the work in the SWISS-MODEL team to fix those issues.