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SWISS-MODEL / covid-19-Annotations-on-Structures

Mapping sequence data onto structures for the Covid-19 Biohackathon April 2020
https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Annotations-on-Structures
MIT License
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Process glycosylation sites to map onto structures #11

Open gtauriello opened 4 years ago

gtauriello commented 4 years ago

Goal is to process glycosylation sites and map expected changes of accessibility onto the structures (see here, here, here and here for work on this).

One option is to use the GlyConnect SARS-CoV-2 page and their API. Example JSON output exists for HEK293 or BTI-Tn-5B1-4.

gtauriello commented 4 years ago

It might also be worth scanning the NAG-ligands in the various experimental structures which are already available: here the current list: 6w41, 6vyb, 6vxx, 6vsb, 6vw1, 6m17, 6m0j, 6lzg

The links above are for the entries in SWISS-MODEL. One could also use the PDB-data directly but the SWISS-MODEL may have a convenient processing of the data by splitting it into biological assemblies and conveniently grouping all ligands into a single chain named '_'.

As a side note: the publication for 6W41 marks their N-glycosylation site as an interesting difference to SARS-CoV with respect to its potential interaction with a SARS-CoV-antibody.

D-Barradas commented 4 years ago

Ok, @gtauriello do you have a particular tool in mind to do the scanning?

gtauriello commented 4 years ago

We use OpenStructure for this type of thing (disclaimer: it's our own in-house framework). It should be easy to use via Docker or Singularity containers. But it's of course ok to use any tool you are more familiar with. My colleague is currently finishing an example script which processes structures into annotations with OpenStructure and will add it to this repo (part of issue #20 ). Doing queries of the structural neighborhood of atoms is very easy in that framework.

schdaude commented 4 years ago

FYI: Yesterday I added example code using a distance query in OpenStructure. The code is available in the wiki.

mlgill commented 4 years ago

Opened a WIP PR here: #35

Tried to add the "in progress" label, but it doesn't seem that I can do so.

glycosciences commented 4 years ago

I have a first model with glycans available (will need some improvements, but can serve as a proof of concept), but I cannot push the commit.

mlgill commented 4 years ago

@glycosciences OK, I'm finishing work on another task so I'll hold off on this until we've discussed.

Feel free to ask in the Slack channel if you think the issues are git related and need some tips.

gtauriello commented 4 years ago

Great news: the glycosylated SARS-CoV-2 spike protein by Oliver Grant in the Woods lab is publicly available now here: https://modelarchive.org/doi/10.5452/ma-zykoq (preprint of the work is available here). I think this will be very valuable here...

mlgill commented 4 years ago

@glycosciences @gtauriello Had several interruptions today, so still finishing up a previous PR. If you'll update this thread with any needed assistance, I'll see if I can help tomorrow.

gtauriello commented 4 years ago

An additional source of information is here: https://cen.acs.org/biological-chemistry/proteomics/Adding-missing-sugars-coronavirus-protein/98/i16