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DNA Motif Contact Count
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evo-design/proto-language/proto_language/constraint/protein_structure/dna_motif_contact_constraint.py
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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.

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API Reference

ConfigDNAMotifContactCountConfig Source
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.
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List[integer]
required
0-based motif indices on the selected DNA chain.
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integer
default:"0"
Index of DNA chain in order-of-appearance in the PDB (0-based).
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integer
default:"1"
Minimum motif-local protein-DNA residue-pair contacts required.
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integer
default:"1"
Minimum number of unique contacting protein residues.
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integer
default:"1"
Minimum number of motif DNA positions with at least one contact.
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number
default:"4.0"
Heavy-atom distance cutoff for contact detection.
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enum
default:"base"
Which DNA atoms are considered for motif contacts.Options: base, any, backbone
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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-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.

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Usage

python

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Metadata