sokrypton / sokrypton/ColabFold
How to predict the structure of cyclic peptides?
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
I have a cyclic peptide sequence. I put it into Alphafold2 Colab, but I didn't get a cyclic peptide structure. What should I do to connect the C-terminal and N-terminal for the next dynamic simulation (GROMACS)?
Should I do some processing on the structure obtained by Alphafold2 Colab for Gromacs dynamics? Or input sequence to Alphafold2 Colab need for some pre-processing? Or can Alphafold2 not predict the sequence of cyclic peptides?
It's really important for my research, thanks for any help.
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 files, tests, or entry points are mentioned. Start by reviewing how ColabFold/AlphaFold2 handles cyclic peptide sequences and how the resulting structure can be prepared for GROMACS; done means documenting a reproducible workflow or clearly stating the supported limitations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, documentation, machine-learning
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100