Structure Interface pLDDT

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

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@article{jumper2021alphafold2,
  title={Highly accurate protein structure prediction with AlphaFold},
  author={Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
  journal={Nature},
  volume={596},
  number={7873},
  pages={583--589},
  year={2021},
  publisher={Nature Publishing Group},
  doi={10.1038/s41586-021-03819-2}
}

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Constraint contributors

Evaluate AF2 binder interface pLDDT confidence. This reads the predictor-style iplddt metric exposed through the AF2 binder adapter and returns 1.0 - iplddt so lower scores indicate better interface-local confidence. The underlying ColabDesign objective is still preserved separately as loss_iplddt metadata.

API Reference

ConfigStructureBasedConstraintConfig Source

Base configuration for constraints using structure prediction tools.This base class standardizes how structure prediction tools and their configurations are specified across all structure-based constraints. Each tool has its own dedicated config field.Subclasses can optionally restrict which tools are supported by overriding the structure_tool field with a narrower Literal type.

enum

default:"esmfold"

Predictor: esmfold/esmfold2/alphafold3/boltz2/chai1/protenix/alphafold2/alphafold2_binder.Options: esmfold, esmfold2, alphafold3, boltz2, chai1, protenix, alphafold2, alphafold2_binder

ESMFoldConfig

Configuration for ESMFold structure prediction.

ESMFold2Config

Configuration for ESMFold2 structure prediction.

AlphaFold3Config

Configuration for AlphaFold3 structure prediction.

Boltz2Config

Configuration for Boltz2 structure prediction.

Chai1Config

Configuration for Chai1 structure prediction.

ProtenixConfig

Configuration for Protenix structure prediction.

AlphaFold2Config

Configuration for the general AlphaFold2 multimer structure predictor.

AlphaFold2BinderStructureConfig

Configuration for the AF2 binder-design backend.

ReturnsConstraintOutput

Per-proposal interface pLDDT confidence scores.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import structure_iplddt_constraint, StructureBasedConstraintConfig

constraint = Constraint(
    inputs=[segment],
    function=structure_iplddt_constraint,
    function_config=StructureBasedConstraintConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	`structure-iplddt`
Function	`structure_iplddt_constraint`
Category	`protein_structure`
Mode	`discrete`
Uses GPU	`True`
Supported Types	`protein`

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Structure Interface pLDDT

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