sokrypton / sokrypton/ColabFold
Using embeddings (single residue and pairwise)
Open
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
How can I connect the embedding to the original sequence?
For example, for the input sequence of 120 residues I got a single residue embedding of 132x384.
Does it include insertions in the MSA?
Thanks!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue mentions a 120-residue input, a 132x384 single-residue embedding, and possible MSA insertions, but names no file or test. Trace where these embeddings are produced and document how embedding positions map to the original sequence, including whether MSA insertions are included.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100