Structure Radius Gyration

Evaluate AF2 radius-of-gyration loss.

License: AlphaFold2 uses Apache-2.0 for code and CC-BY-4.0 for model weights and may require explicit attribution when utilized. Please refer to the code license and model weights license 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.

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proto-bio/proto-language/proto_language/constraint/protein_structure/structure_geometry_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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Evaluate AF2 binder radius-of-gyration loss.

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.

structure_tool · enum · default: "esmfold"

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

Options: esmfold, esmfold2, alphafold3, boltz2, chai1, protenix, alphafold2, alphafold2_binder

esmfold_config · ESMFoldConfig

Configuration for ESMFold structure prediction.

esmfold2_config · ESMFold2Config

Configuration for ESMFold2 structure prediction.

alphafold3_config · AlphaFold3Config

Configuration for AlphaFold3 structure prediction.

boltz2_config · Boltz2Config

Configuration for Boltz2 structure prediction.

chai1_config · Chai1Config

Configuration for Chai1 structure prediction.

protenix_config · ProtenixConfig

Configuration for Protenix structure prediction.

alphafold2_config · AlphaFold2Config

Configuration for the general AlphaFold2 multimer structure predictor.

alphafold2_binder_config · AlphaFold2BinderStructureConfig

Configuration for the AF2 binder-design backend.

ReturnsConstraintOutput

Raw AF2 rg loss outputs.

Usage

python

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

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	structure-radius-gyration
Function	structure_radius_gyration_constraint
Category	protein_structure
Mode	discrete
Uses GPU	True
Supported Types	protein