> ## 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. # AF3 Chain-Pair Protein-DNA ipTM > Score protein-DNA interface confidence using the chain-pair ipTM matrix, returning the max (or mean) ipTM across all protein-DNA chain pairs.
AF3 Chain-Pair Protein-DNA ipTM
**License:** This constraint can use multiple tools, each under its own license. See the **Tools Used** tab and each tool's page for license details.

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.

evo-design/proto-language/proto\_language/constraint/protein\_structure/af3\_chain\_pair\_prot\_dna\_iptm\_constraint.py
View source
Constraint contributors
Score protein-DNA ipTM from a per-chain-pair ipTM matrix. For each candidate complex: 1. Separate protein and DNA sequences from the input tuple. 2. Build a complex with `num_protein_copies` protein chains and all DNA chains (optionally adding the reverse complement). 3. Run the configured structure predictor and read `chain_pair_iptm`. 4. Pick out the protein-to-DNA entries and aggregate (max or mean). 5. Score: 0.0 (best) when aggregated ipTM >= `desired_iptm`, 1.0 (worst) when ipTM is 0. When the predictor does not expose the per-chain-pair ipTM matrix this raises `RuntimeError`: overall ipTM is not a valid substitute. **Supported tools**: any DNA-capable `StructureBasedConstraintConfig` predictor; AlphaFold3 and Protenix emit the per-chain-pair ipTM matrix under `chain_pair_iptm`, and Boltz-2 emits the same matrix under `pair_chains_iptm`. ## API Reference
ConfigAF3ChainPairProtDNAIPTMConfig Source
Config for the AF3 chain-pair protein-DNA ipTM constraint. Runs a structure prediction for the protein-DNA complex and extracts the pairwise chain ipTM matrix. Only the protein-to-DNA entries are kept; the result is aggregated via `aggregation` (default: max over all protein-DNA chain pairs — both dimer halves, and both DNA strands when `include_reverse_complement` is set), then scored against `desired_iptm`. The per-chain-pair ipTM matrix (`chain_pair_iptm`) is exposed by both AlphaFold3 and Protenix. Boltz-2 exposes the same matrix under `pair_chains_iptm`. A tool that does not surface the matrix raises a `RuntimeError` — overall ipTM is not a valid substitute. Protein monomer copies in the complex (2=homodimer, 1=monomer); reuses input chains first. Interface scored: 'protein-dna' (protein-DNA ipTM) or 'protein-protein' (homodimer ipTM). Options: `protein-dna`, `protein-protein` Target protein-DNA chain-pair ipTM. Score is 0 when achieved. Aggregate protein-DNA chain-pair ipTM: 'max' (best pair) or 'mean' (average of pairs). Options: `max`, `mean` Add the reverse-complement DNA strand when the input has only one DNA sequence. 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) with `prot_dna_iptm` / `prot_prot_iptm` / `overall_iptm` metadata and the predicted Structure on slot 0.
## Usage Programming a protein-DNA operator complex with Protenix: ```python python icon="python" theme={null} >>> from proto_language.core import Segment >>> protomer = Segment(length=120, sequence_type="protein") >>> operator = Segment(length=20, sequence_type="dna") >>> chain_pair_iptm = Constraint( ... inputs=[protomer, operator], ... function=af3_chain_pair_prot_dna_iptm_constraint, ... function_config={"structure_tool": "protenix", "num_protein_copies": 2}, ... ) ``` ## Metadata | Property | Value | | --------------- | ----------------------------------------- | | Key | `af3-chain-pair-prot-dna-iptm` | | Function | `af3_chain_pair_prot_dna_iptm_constraint` | | Category | `protein_structure` | | Mode | `discrete` | | Uses GPU | `True` | | Supported Types | `protein`, `dna` |