Structural RMSD Similarity

Compare structure RMSD against a target (PDB or Sequence) using generic predictors.

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.

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Tools Used Tools Used Source Source

Structure Prediction · 7 tools

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

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Predicts structure of input proposals and compares RMSD against a target.

Returns a score 0-1 (0 is perfect match). Metadata describes the predicted full input tuple/complex, not an individual chain.

API Reference

ConfigStructureRMSDConfig Source

Configuration for RMSD-based structure similarity.

This configuration extends StructureSimilarityConfig with specific parameters for calculating the Root Mean Square Deviation (RMSD) between the target and proposal structures. The raw RMSD value is transformed into a 0-1 constraint score using a sigmoid function, where 0 represents a perfect match (low RMSD) and 1 represents a poor match (high RMSD).

Inherits target specification (target_chains, target_structure, min_target_plddt) from StructureSimilarityConfig and tool selection (structure_tool, esmfold_config, esmfold2_config, alphafold3_config, boltz2_config, chai1_config, protenix_config, alphafold2_config, alphafold2_binder_config) from StructureBasedConstraintConfig.

inflection_point_angstroms · number · default: "2.0"

RMSD in Ångströms where the sigmoid score equals 0.5; values below 2 Å are generally a good match.

sigmoid_slope · number · default: "3.0"

Steepness of the penalty curve.

pymol_alignment_method · enum · default: "cealign"

PyMOL alignment routine for RMSD calculation.

Options: cealign, align

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.

target_chains · array | Complex

Target chains: a tuple of sequence strings (entity types auto-detected).

target_structure · Structure | string

Target structure: a Structure object, file path (.pdb/.cif), or raw PDB/CIF content string.

min_target_plddt · number · default: "0.6"

Min mean pLDDT (0-1 scale) for a target folded from sequence; ignored when target_structure is set.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import structure_rmsd_constraint, StructureRMSDConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	structure-rmsd
Function	structure_rmsd_constraint
Category	protein_structure
Mode	discrete
Uses GPU	True
Supported Types	protein, rna, dna, ligand