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Structural TM-score Similarity
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Structure Prediction · 7 tools
evo-design/proto-language/proto_language/constraint/protein_structure/structure_similarity_constraint.py
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Constraint contributors
Predicts structure and compares TM-score. Returns (1.0 - TMscore). This constraint automatically selects the appropriate alignment tool based on the oligomer state of the inputs:
  • Monomer vs monomer comparisons use standard TMalign.
  • Comparisons involving multiple chains use USalign with -mm 1 and default values for all other parameters.
The two raw TM-scores are combined per config.tm_score_normalization (default: arithmetic mean of the proposal- and target-normalized scores); the target is the reference structure. Metadata describes the predicted full input tuple/complex, not an individual chain.

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API Reference

ConfigStructureTMScoreConfig Source
Configuration for TM-score based structure similarity.This configuration extends StructureSimilarityConfig for calculating the Template Modeling score (TM-score) between the target and proposal structures. TM-score is a metric for assessing the topological similarity of protein structures and is less sensitive to local variations than RMSD.The constraint returns a score calculated as (1.0 - TM_score), where 0.0 indicates a perfect match (TM-score = 1.0) and values closer to 1.0 indicate poor structural similarity.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.
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number
Drop residues with pLDDT (0-100 scale, in B-factor) below this before alignment; None keeps all.
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enum
default:"mean"
How to combine the two TM-scores from TM-align/US-align: structure1, structure2, max, min, or mean.Options: structure1, structure2, max, min, mean
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enum
default:"esmfold"
Predictor: esmfold/esmfold2/alphafold3/boltz2/chai1/protenix/alphafold2/alphafold2_binder.Options: esmfold, esmfold2, alphafold3, boltz2, chai1, protenix, alphafold2, alphafold2_binder
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ESMFoldConfig
Configuration for ESMFold structure prediction.
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ESMFold2Config
Configuration for ESMFold2 structure prediction.
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AlphaFold3Config
Configuration for AlphaFold3 structure prediction.
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Boltz2Config
Configuration for Boltz2 structure prediction.
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Chai1Config
Configuration for Chai1 structure prediction.
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ProtenixConfig
Configuration for Protenix structure prediction.
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AlphaFold2Config
Configuration for the general AlphaFold2 multimer structure predictor.
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AlphaFold2BinderStructureConfig
Configuration for the AF2 binder-design backend.
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array | Complex
Target chains: a tuple of sequence strings (entity types auto-detected).
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Structure | string
Target structure: a Structure object, file path (.pdb/.cif), or raw PDB/CIF content string.
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number
default:"0.6"
Min mean pLDDT (0-1 scale) for a target folded from sequence; ignored when target_structure is set.

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Usage

python

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Metadata