Scoping visualising protein structure in the FE

[carcruz]

The requirements could be:

• Loading pdb structures - ideally from a remote server and not locally
• Ability to interact with the structure (panning, zooming, etc.) - Ideally the interaction should not trigger while scrolling the page.
• Ability to highlight individual residues based on provided coordinates (one or several) (e.g. variants)
• Ability to highlight areas (pockets)
• Avoid heavy libraries, we just want basic usage.

Some sites visualising structures:

• AlphaFoldDB - https://alphafold.ebi.ac.uk/entry/A0A809NQF6
• PDBe - https://www.ebi.ac.uk/pdbe/entry/pdb/2v3o
• RCSB-PDB - https://www.rcsb.org/3d-view/2V3O
• ProtVar
• mutfunc
• protvista/web-components - https://github.com/ebi-webcomponents/protvista-uniprot

[d0choa]

In case this helps, requirements would/could be:

• Load pdb structures - ideally from a remote server (not locally).
• Ability to interact with the structure (panning, zooming, etc.)
• Ability to highlight individual residues based on provided coordinates (one or several) (e.g. variants)
• Ability to highlight areas (pockets)
• Avoid heavy libraries, we just want basic usage.

Some sites visualising structures (alphafolddb, pdbe, rcsb-pdb, ProtVar, mutfunc, protvista/web-components, ...)

[gjmcn]

The Nightingale components that protvista-uniprot is build with seem to satisfy the requirements - 'pockets' may take some work.

Here's an example of loading only the 3D structure: https://ebi-webcomponents.github.io/nightingale/?path=/story/components-structure--structure

@carcruz are there issues with using protvista on the platform that prompted this ticket?

[d0choa]

The context is that we have upcoming data on visualising data structures and we might need to enhance our game on visualising 3d structures.

I had a few chats with other teams and it looks like the gold standard at the moment is Mol*. One of the developers is currently at EBI for a few months and it would be a good opportunity to establish a collaboration. The ProtVar team has been using it successfully, but they had to implement a few things on top to make it work for their use case.

In terms of actions, it would be good to see if Mol* sits well in our application (react compatibility etc.). What kind of inputs requires, etc. It would help to scope further development of the required data during the summer.

[gjmcn]

In addition to the Nightingale components mentioned above, Mol* itself has a JS API and a React-based UI where "Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions". I will take look at how well suited any of these are for use in the platform.