Structure Interface Contact

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

evo-design/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

Constraint contributors

Evaluate AF2 binder interface 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.

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

Raw AF2 i_con loss outputs.

Usage

python

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

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

scores = constraint.evaluate()

Metadata

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

Language

Language Concepts

Language Guides

Constraints

Generators

Optimizers

Structure Interface Contact

API Reference

Usage

Metadata

​API Reference

​Usage

​Metadata

API Reference

Usage

Metadata