RosettaCommons / RosettaCommons/RFdiffusion

Question Regarding the Use of Hotspot Option in Motif Scaffolding

Open
#178 0 comments 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
3.1k
Forks
644
PR merge metrics
No merged PRs in 30d

Description

Hello, thank you for creating such a great model.
I am currently redesigning part of an existing Binder.
My task involves designing a portion of Chain B, while Chain A remains fixed. I've utilized motif scaffolding and incorporated some residues of Chain A as hotspots.
I entered it as follows :
'contigmap.contigs=[A1-224/0 B1-97/'"${k}"'-'"${k}"'/B105-116]' 'ppi.hotspot_res=[A139,A141,A142,A199,A201]'

My question is this:
How can I confirm whether RFdiffusion is actually incorporating these hotspots in the design?

I indirectly verified that the Hotspot option wasn't ignored because the log shows that 'Complex_base_ckpt.pt' is being used.
Screen Shot 2023-12-21 at 4 38 57 PM

However, since all example Binder designs are about designing an entirely new Chain, I'm not sure if my input script is working as intended. I'm quite new to this field and not yet proficient in reading code.
Can RFdiffusion operate in the way I intend? Or is there another method to check whether hotspots are being used?

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Review the motif-scaffolding and binder-design examples alongside the contigmap.contigs and ppi.hotspot_res arguments. Compare the fixed Chain A and designed Chain B setup with those examples, then inspect the run log's Complex_base_ckpt.pt entry. Done means documenting whether this input mode supports hotspots and a reproducible check that confirms their use.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Documentation
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.