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backbone with clashes

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Assessment

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

Research direction

Run the stated python sampling command and inspect the generated PDB structures for steric clashes. Investigate whether backbone reconstruction from angles, training, model mode, or data explains the observations. Done would require identifying the source of the clashes, but the issue does not specify a target fix or test.

Written by the indexing model from the issue text.

Description

Hi,

Very interesting work.

I tried the sampling command 'python ~/projects/foldingdiff/bin/sample.py -l 50 128 -n 10 -b 512 --device cuda:0' and I observed a lot of steric clashes within the generated PDB structures. Any insights about where these clashes might come from? Based on the paper, it seems rebuilding the backbone from angles does not really cause problems. So it could be the training/mode/data?

Best,
Xiaotong

Dominant language
Jupyter Notebook
Stars
568
Forks
74
Avg merge
20h 2m
Merged PRs (30d)
1

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