OpenFreeEnergy / OpenFreeEnergy/openfe
Protein-Protein or Protein-Peptide alchemistry?
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Dear OpenFE team.
Thanks for this awesome work.
This is related to https://github.com/OpenFreeEnergy/openfe/issues/633 https://github.com/OpenFreeEnergy/openfe/issues/634 and https://github.com/OpenFreeEnergy/openfe/issues/636
I would like to start with a protein-peptide co-crystal structure and modify the peptide by
- doing amino acid mutations
- adding small groups like methyl, acetyl etc.
Are there any special instructions for doing such calculations or should I treat my peptide as a small molecule and follow the lysozyme-benzene tutorial?
I would be really grateful for any suggestions.
Best,
Amin.
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 reading issues 633, 634, and 636, then review the lysozyme-benzene tutorial mentioned in the question. Determine whether protein-peptide mutations and small-group additions need dedicated instructions or can follow the small-molecule workflow; done means documenting a clear supported workflow.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100