> ## 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 Motif Contact Count
> Require motif-local protein-DNA contacts in predicted complexes
**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 motif-local protein-DNA contact deficits in predicted complexes.
Predicts (or reuses) one protein-DNA complex per proposal, parses the PDB
geometry, and counts heavy-atom contacts between protein residues and the
selected DNA motif. The score is the largest of three normalized deficits
(contact pairs, unique protein residues, unique DNA positions), so `0` is
best (all minimum requirements met) and `1` is worst.
## API Reference
Configuration for the dna-motif-contact-count constraint.
Predicts (or reuses) a protein-DNA complex and counts heavy-atom contacts
between protein residues and a selected DNA motif. The score is the largest
of three normalized deficits (contact pairs, unique protein residues, unique
DNA positions) clamped to `[0, 1]`, where `0` means every minimum
requirement is met and `1` means none are.
0-based motif indices on the selected DNA chain.
Index of DNA chain in order-of-appearance in the PDB (0-based).
Minimum motif-local protein-DNA residue-pair contacts required.
Minimum number of unique contacting protein residues.
Minimum number of motif DNA positions with at least one contact.
Heavy-atom distance cutoff for contact detection.
Which DNA atoms are considered for motif contacts.
Options: `base`, `any`, `backbone`
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-proposal score in `[0, 1]` (lower is
better) and metadata describing the motif contacts (counts, the
selected DNA chain, motif indices, cutoff, and resolved PDB path).
A proposal whose structure shape prevents scoring (no DNA chains, no
DNA residues, out-of-range `dna_chain_label` or `dna_indices`)
soft-fails to `MAX_ENERGY` with `motif_contact_error` metadata.
evo-design/proto-language/proto\_language/constraint/protein\_structure/dna\_motif\_contact\_constraint.py
