Class: ProteinStructure

A 3D protein structure from PDB or AlphaFold relevant to understanding a treatment's mechanism of action. Enables embedded 3D visualization of drug-target interactions via Mol* viewer.

URI: dismech:class/ProteinStructure

 classDiagram
    class ProteinStructure
    click ProteinStructure href "../../classes/ProteinStructure/"
      ProteinStructure : description

      ProteinStructure : ligand

      ProteinStructure : method

      ProteinStructure : pdb_id

      ProteinStructure : publication

      ProteinStructure : resolution_angstrom

      ProteinStructure : target_protein

Slots

Name	Cardinality and Range	Description	Inheritance
pdb_id	1 String	PDB accession code (e	direct
description	0..1 String	Brief description of what the structure shows (e	direct
resolution_angstrom	0..1 Float	Structure resolution in angstroms (for experimental structures)	direct
method	0..1 String	Experimental method (X-ray, cryo-EM, NMR) or prediction method (AlphaFold)	direct
ligand	0..1 String	Name of bound drug/ligand if this is a co-crystal structure	direct
target_protein	0..1 String	Name of the protein target in the structure	direct
publication	0..1 PMID	Reference for the structure deposition or associated paper (e	direct

Usages

used by	used in	type	used
Pathophysiology	pdb_structures	range	ProteinStructure
Treatment	pdb_structures	range	ProteinStructure

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type	Mapped Value
self	dismech:ProteinStructure
native	dismech:ProteinStructure

LinkML Source

Direct

name: ProteinStructure
description: A 3D protein structure from PDB or AlphaFold relevant to understanding
  a treatment's mechanism of action. Enables embedded 3D visualization of drug-target
  interactions via Mol* viewer.
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  pdb_id:
    name: pdb_id
    description: PDB accession code (e.g., 3TCT) or AlphaFold identifier (e.g., AF-P02766-F1).
      Used to construct viewer URLs and fetch structure data.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - ProteinStructure
    range: string
    required: true
  description:
    name: description
    description: Brief description of what the structure shows (e.g., drug-target
      co-crystal)
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
  resolution_angstrom:
    name: resolution_angstrom
    description: Structure resolution in angstroms (for experimental structures)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - ProteinStructure
    range: float
  method:
    name: method
    description: Experimental method (X-ray, cryo-EM, NMR) or prediction method (AlphaFold)
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - ProteinStructure
    - AssociationSignal
    - GOEnrichment
    range: string
  ligand:
    name: ligand
    description: Name of bound drug/ligand if this is a co-crystal structure
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - ProteinStructure
    range: string
  target_protein:
    name: target_protein
    description: Name of the protein target in the structure
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - ProteinStructure
    range: string
  publication:
    name: publication
    description: Reference for the structure deposition or associated paper (e.g.,
      PMID:12345678)
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    range: PMID

Induced

name: ProteinStructure
description: A 3D protein structure from PDB or AlphaFold relevant to understanding
  a treatment's mechanism of action. Enables embedded 3D visualization of drug-target
  interactions via Mol* viewer.
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  pdb_id:
    name: pdb_id
    description: PDB accession code (e.g., 3TCT) or AlphaFold identifier (e.g., AF-P02766-F1).
      Used to construct viewer URLs and fetch structure data.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: pdb_id
    owner: ProteinStructure
    domain_of:
    - ProteinStructure
    range: string
    required: true
  description:
    name: description
    description: Brief description of what the structure shows (e.g., drug-target
      co-crystal)
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: description
    owner: ProteinStructure
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
  resolution_angstrom:
    name: resolution_angstrom
    description: Structure resolution in angstroms (for experimental structures)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: resolution_angstrom
    owner: ProteinStructure
    domain_of:
    - ProteinStructure
    range: float
  method:
    name: method
    description: Experimental method (X-ray, cryo-EM, NMR) or prediction method (AlphaFold)
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: method
    owner: ProteinStructure
    domain_of:
    - ProteinStructure
    - AssociationSignal
    - GOEnrichment
    range: string
  ligand:
    name: ligand
    description: Name of bound drug/ligand if this is a co-crystal structure
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: ligand
    owner: ProteinStructure
    domain_of:
    - ProteinStructure
    range: string
  target_protein:
    name: target_protein
    description: Name of the protein target in the structure
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_protein
    owner: ProteinStructure
    domain_of:
    - ProteinStructure
    range: string
  publication:
    name: publication
    description: Reference for the structure deposition or associated paper (e.g.,
      PMID:12345678)
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: publication
    owner: ProteinStructure
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    range: PMID