[SCENE] Antibody contact prediction

[sdvillal]

Braindump WIP

Goals

• Unexplored: how modern DL workflows can predict HCDR3 conformations?
• How meaningful is an MSA for an antibody (vs the importance of MSA in standard protein conformation prediction, e.g. in AlphaFold2)
• Possible Conclusions: promising results, but more work is needed to make this useful in our pipelines

Real data

• Already generated MSAs and contacts for two use cases with ground truth data:
  • 1HZH vaccine template
  • Our internal crystalized AB (for this we can only show contacts and should not put any data in github)

TODO

• [ ] AntibodyMObject (will get from antidoto)
• [ ] MSAMObject

Kinda Storyboard

• Warning: actual computations happened to generate this video
• LoL logo
• Render the 1D chain of the AB in bioviz studio and make it become 3D
• AlphaFold2 watershed moment
• Importance of coevolution (MSA) in AlphaFold2 workflow
• Can it work for antibodies?
• This is an antibody, this is an MSA, these are the predicted contacts
• This is the predicted contact map for an internal Ab, could it have been useful
• What we can do if we get focused work on the topic

[sdvillal]

@ap-- unrelated question, is it not possible anymore to assign more than one person to an issue in GH?

[ap--]

was it ever possible?

[ap--]

Seems like it worked at some point: https://github.blog/2016-05-27-multiple-assignees-on-issues-and-pull-requests/

[ap--]

https://github.com/pricing#compare-features

scroll down to "Multiple Issue Assignees". On the free tier it's only 1 for private repos

[sdvillal]

pity, I guess I was spoiled with paid tiers and public repos... maybe we should just make this repo public already?

(although the ping pong of assignments in this issue is encouraging)

[ap--]