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DNA Phosphate Contact
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 and model weights license for full terms.

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evo-design/proto-language/proto_language/constraint/protein_structure/dna_phosphate_contact_constraint.py
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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.

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API Reference

ConfigDNAPhosphateContactConfig Source
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.
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number
default:"3.5"
Heavy-atom distance cutoff for phosphate contacts.
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integer
default:"2"
Target number of unique phosphate H-bond contacts; 0 score when met.
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List[string]
default:"['OP1', 'OP2', 'O1P', 'O2P']"
DNA backbone phosphate atom names treated as eligible H-bond acceptors (OP1/OP2 + legacy O1P/O2P).
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enum
default:"alphafold3"
Predictor for the protein-DNA complex; must be DNA-capable (alphafold3/boltz2/protenix).Options: esmfold, esmfold2, alphafold3, boltz2, chai1, protenix, alphafold2, alphafold2_binder
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ESMFoldConfig
Configuration for ESMFold structure prediction.
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ESMFold2Config
Configuration for ESMFold2 structure prediction.
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AlphaFold3Config
Configuration for AlphaFold3 structure prediction.
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Boltz2Config
Configuration for Boltz2 structure prediction.
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Chai1Config
Configuration for Chai1 structure prediction.
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ProtenixConfig
Configuration for Protenix structure prediction.
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AlphaFold2Config
Configuration for the general AlphaFold2 multimer structure predictor.
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AlphaFold2BinderStructureConfig
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.

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Usage

python

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Metadata