Metadata-Version: 2.4
Name: alphafold3-polymer-bonds
Version: 0.3
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: CC-BY-NC-SA-4.0
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Requires-Dist: biopython
Requires-Dist: humanfriendly
Requires-Dist: pandas
Requires-Dist: py3dmol
Description-Content-Type: text/markdown

[![PyPI - Version](https://img.shields.io/pypi/v/alphafold3-polymer-bonds)](https://pypi.org/project/alphafold3-polymer-bonds/)
[![PyPI Downloads](https://static.pepy.tech/personalized-badge/alphafold3-polymer-bonds?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/alphafold3-polymer-bonds)

# 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 exploratory, see below for specifc examples. Also take a look at complementary work:
[KosinskiLab/af3x](https://github.com/KosinskiLab/af3x)
and
[bio-phys/polyUb-AF](https://github.com/bio-phys/polyUb-AF).*

![1AAR](examples/visualise/1AAR.png)
1AAR with (left, RMSD<1) vs without (right, RMSD>10) covalent bond between Lys48 and Gly76, AlphaFold3 run without templates

## Quick start
```bash
pip install alphafold3-polymer-bonds
alphafold3_polymer_bonds --help
```

