> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# DNA Phosphate Contact
> Score protein-DNA backbone phosphate H-bond contacts from PDB geometry. Mirrors the AlphaFold3 phosphate-contact H-bond term, rewarding protein polar sidechain contacts to DNA phosphate oxygens (optionally weighted by residue type). Does not require Rosetta relaxation.
**License:** AlphaFold3 uses Apache-2.0 for code and Custom (AlphaFold 3 Model Parameters Terms of Use) for model weights and has restrictions around commercial use and may require explicit attribution when utilized. Model weights are not publicly distributed and must be requested from the provider. Please refer to the [code license](https://github.com/google-deepmind/alphafold3/blob/main/LICENSE) and [model weights license](https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md) for full terms.
This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.
```bibtex theme={null}
@article{abramson2024alphafold3,
title={Accurate structure prediction of biomolecular interactions with AlphaFold 3},
author={Abramson, Josh and Adler, Jonas and Dunger, Jack and Evans, Richard and Green, Tim and Pritzel, Alexander and Ronneberger, Olaf and Willmore, Lindsay and Ballard, Andrew J and Bambrick, Joshua and others},
journal={Nature},
volume={630},
number={8016},
pages={493--500},
year={2024},
publisher={Nature Publishing Group},
doi={10.1038/s41586-024-07487-w}
}
```
Score protein-DNA phosphate contacts from a predicted complex PDB.
Resolves (reuses or predicts) a protein-operator complex PDB per candidate
tuple, then counts protein polar sidechain H-bond contacts to DNA backbone
phosphate oxygens directly from heavy-atom geometry. The score is 0 when the
integer phosphate-contact count meets the target and rises toward 1 as it
falls short, mirroring the base-contact-quality penalty mapping.
## API Reference
Config for geometry-based DNA phosphate contact scoring.
Scores protein-DNA complexes based on protein polar side-chain H-bond
contacts to DNA backbone phosphate oxygens, measured directly from
heavy-atom distances in a predicted complex PDB without requiring Rosetta
relaxation. Mirrors the AlphaFold3 phosphate-contact H-bond term (separate
from the base-contact H-bond term). Inherits the structure-prediction tool
selection and per-tool configs from `StructureBasedConstraintConfig`.
Heavy-atom distance cutoff for phosphate contacts.
Target number of unique phosphate H-bond contacts; 0 score when met.
DNA backbone phosphate atom names treated as eligible H-bond acceptors (OP1/OP2 + legacy O1P/O2P).
Predictor for the protein-DNA complex; must be DNA-capable (alphafold3/boltz2/protenix).
Options: `esmfold`, `esmfold2`, `alphafold3`, `boltz2`, `chai1`, `protenix`, `alphafold2`, `alphafold2_binder`
Configuration for ESMFold structure prediction.
Configuration for ESMFold2 structure prediction.
Configuration for AlphaFold3 structure prediction.
Configuration for Boltz2 structure prediction.
Configuration for Chai1 structure prediction.
Configuration for Protenix structure prediction.
Configuration for the general AlphaFold2 multimer structure predictor.
Configuration for the AF2 binder-design backend.
ReturnsConstraintOutput
Per-candidate score in `[0, 1]` (lower is
better) with phosphate-contact metadata (`n_phosphate_contacts`,
`weighted_phosphate_score`, `n_unique_residues`,
`contacting_types`, and `pdb_path`). Candidates whose structure
could not be resolved receive `MAX_ENERGY`.
evo-design/proto-language/proto\_language/constraint/protein\_structure/dna\_phosphate\_contact\_constraint.py
