Metadata-Version: 2.4
Name: alphafold3-polymer-bonds
Version: 0.1
Summary: Support for covalent bonds between/within polymer chains (protein, DNA, RNA) in AlphaFold3
Project-URL: Homepage, https://github.com/jurgjn/alphafold3-polymer-bonds
Project-URL: Issues, https://github.com/jurgjn/alphafold3-polymer-bonds/issues
Author-email: jurgjn <jurgjn@users.noreply.github.com>
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Requires-Dist: biopython
Requires-Dist: pandas
Description-Content-Type: text/markdown

# Polymer bonds in AlphaFold3
AlphaFold3
[does not allow](https://github.com/google-deepmind/alphafold3/blob/main/docs/input.md#bonds)
covalent bonds between/within polymer chains (protein, DNA, RNA).
We work around this limitation by treating one of the corresponding residue or nucleic acid as a modified residue/amino-acid.
In principle, this may enable AlphaFold3 to explicitly model e.g. disulfide bonds, cyclic peptides, zero-length crosslinkers, protein-DNA bonds..

*This is currently experimental/work-in-progress, please also have a look at complementary approaches
[KosinskiLab/af3x](https://github.com/KosinskiLab/af3x)
and
[bio-phys/polyUb-AF](https://github.com/bio-phys/polyUb-AF).*

## Quick start
```bash
git clone git@github.com:jurgjn/alphafold3-polymer-bonds.git
cd alphafold3-polymer-bonds
pip install -e .
```