sokrypton / sokrypton/ColabFold
AlphaFold2_batch could only take monomer prediction
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hi all,
Thanks for making alphafold2 easily accesible!
While I was running alphafold2_batch, I noticed that no matter how I put the input fasta files, it will only process the first chain and discard other chains.
Is there a workaround or easy fix that could enable it to predict complex which has multiple chains?
Thanks very much!
Ruizhi
example of my fasta file
chain_A
GGGGGGGGGG
chain_B
GGGGGGGGGGGGGGGGGGGGGG
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
Start by reproducing alphafold2_batch with the provided multi-chain FASTA example, then trace how its input is parsed and how chains are selected. Done means a FASTA containing multiple chains processes all chains for complex prediction rather than discarding every chain after the first.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100