sokrypton / sokrypton/ColabFold
How to dock peptide to protein with ColabFold
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- Jupyter Notebook
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Description
Hi,
Suppose I have a Peptide IQGLSFDIYEALL which I want to dock (create a heterocomplex?)
to a protein QEEACAKNFGAFCVFVGIVRKEDN
Is this syntax correct to run with AlphaFold2_advanced ?
QEEACAKNFGAFCVFVGIVRKEDN:IQGLSFDIYEALL
Notice the colon (:)
Especially in the sequence entry. For homooligomer entry I simply leave it as it is.
Thanks and hope to hear from you again.
G.V.
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 with the linked AlphaFold2_advanced notebook, focusing on the sequence and homooligomer inputs. Verify how the notebook documents peptide–protein heterocomplex sequences, then clarify the accepted syntax and expected result for the example in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100