sokrypton / sokrypton/ColabFold
tricking alphafold2 docker to use the same reference sequences as mmseq2
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hi, I've been running the MMseq2 ColabFold for a specific type of protein sequences, and I always get the same set of ~4000 sequences in the .a3m file. Would it be possible to put these sequences from the .a3m file in a file in one of the folders for the local installation of AlphaFold2, and tricking AlphaFold2 to always look at these when running?
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
No file, test, or entry point is named. Start by comparing the MMseq2 ColabFold .a3m output with the local AlphaFold2 installation folders and determine whether the referenced sequences can be supplied there. Done would be a documented, reproducible workflow or a clear explanation of the limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100