Structure Contact Loss

Evaluate AF2 intra-chain contact 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.

---

Tools Used Tools Used Source Source Cite Cite

Go to Tool Page

proto-bio/proto-language/proto_language/constraint/protein_structure/structure_geometry_constraint.py

View source

@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}
}

Copy citation

Evaluate AF2 binder intra-chain contact 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 con loss outputs.

Usage

python

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

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	structure-contact
Function	structure_contact_constraint
Category	protein_structure
Mode	discrete
Uses GPU	True
Supported Types	protein