Review PDB - GlyGen integration

[ReneRanzinger]

Hi Raja,

Please feel free to pass this information to your team.

I would like to let you know that RCSB PDB is currently implementing cross-reference of glycoproteins from RCSB.org to GlyGen resource. This is in addition to cross-referencing glycans to GlyGen resource that was already implemented several years ago.

For example, PDB entry 7xiw will have spike glycoprotein cross-referencing to GlyGen annotation, https://glygen.org/protein/P0DTC2-1 in addition to the disaccharide cross-referencing to GlyGen annotation at https://www.glygen.org/glycan/G42666HT as shown below.

It would be great to get your or your team's feedback on this during this implementation. Let me know if you need more information about this work.

Looking forward to hearing from you or your team!

[ReneRanzinger]

@jeet-vora and @katewarner will review and suggest changes on GlyGen and PDB

[ReneRanzinger]

Hi Raja,

I am copying Yana Valasatava here who is our project manager for RCSB PDB website development.

Here is the URL that your group can play with the GlyGen cross-referencing from RCSB PDB website for glycoproteins:

https://glygen-dev.rcsb.org

For examples,

Example: https://glygen-dev.rcsb.org/structure/7xiw#entity-1 
With symmetry: https://glygen-dev.rcsb.org/structure/1ao5#entity-1

A link to GlyGen is added to the entity summery and a Glycosylation option to see data in 3D view:

You can try with any PDB entry containing glycoprotein (e.g., you can type a PDB ID or UNP ID from the top bar text search).

It would great to get your team's feedback by the end of May, if possible.

We are looking forward to receiving feedback from your team.

Regards,

Jasmine

[katewarner]

Integrating PDBe glycoconjugate information #1459