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