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Class: ConformationalEnsemble

Ensemble of conformational states for a protein

URI: lambdaber:ConformationalEnsemble

classDiagram class ConformationalEnsemble click ConformationalEnsemble href "../ConformationalEnsemble/" NamedThing <|-- ConformationalEnsemble click NamedThing href "../NamedThing/" ConformationalEnsemble : clustering_method ConformationalEnsemble : conformational_states ConformationalEnsemble --> "*" ConformationalState : conformational_states click ConformationalState href "../ConformationalState/" ConformationalEnsemble : description ConformationalEnsemble : energy_landscape ConformationalEnsemble : id ConformationalEnsemble : principal_motions ConformationalEnsemble : protein_id ConformationalEnsemble : rmsd_threshold ConformationalEnsemble : title ConformationalEnsemble : transition_pathways

Inheritance

Slots

Name Cardinality and Range Description Inheritance
protein_id 1
String		 UniProt accession direct
conformational_states *
ConformationalState		 Individual conformational states direct
clustering_method 0..1
String		 Method used for conformational clustering direct
rmsd_threshold 0..1
Float		 RMSD threshold for clustering (Angstroms) direct
transition_pathways 0..1
String		 Description of transition pathways between states direct
energy_landscape 0..1
String		 Description of the energy landscape direct
principal_motions *
String		 Description of principal motions direct
id 1
Uriorcurie		 Globally unique identifier as an IRI or CURIE for machine processing and exte... NamedThing
title 0..1
String		 A human-readable name or title for this entity NamedThing
description 0..1
String		 A detailed textual description of this entity NamedThing

Usages

used by used in type used
Sample conformational_ensemble range ConformationalEnsemble
AggregatedProteinView conformational_ensemble range ConformationalEnsemble

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:ConformationalEnsemble
native lambdaber:ConformationalEnsemble

LinkML Source

Direct

name: ConformationalEnsemble
description: Ensemble of conformational states for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  protein_id:
    name: protein_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    required: true
  conformational_states:
    name: conformational_states
    description: Individual conformational states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    range: ConformationalState
    multivalued: true
    inlined: true
    inlined_as_list: true
  clustering_method:
    name: clustering_method
    description: Method used for conformational clustering
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  rmsd_threshold:
    name: rmsd_threshold
    description: RMSD threshold for clustering (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    range: float
    unit:
      ucum_code: Angstrom
  transition_pathways:
    name: transition_pathways
    description: Description of transition pathways between states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  energy_landscape:
    name: energy_landscape
    description: Description of the energy landscape
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  principal_motions:
    name: principal_motions
    description: Description of principal motions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    multivalued: true

Induced

name: ConformationalEnsemble
description: Ensemble of conformational states for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  protein_id:
    name: protein_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: protein_id
    owner: ConformationalEnsemble
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    range: string
    required: true
  conformational_states:
    name: conformational_states
    description: Individual conformational states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conformational_states
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: ConformationalState
    multivalued: true
    inlined: true
    inlined_as_list: true
  clustering_method:
    name: clustering_method
    description: Method used for conformational clustering
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: clustering_method
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  rmsd_threshold:
    name: rmsd_threshold
    description: RMSD threshold for clustering (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: rmsd_threshold
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: float
    unit:
      ucum_code: Angstrom
  transition_pathways:
    name: transition_pathways
    description: Description of transition pathways between states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: transition_pathways
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  energy_landscape:
    name: energy_landscape
    description: Description of the energy landscape
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: energy_landscape
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  principal_motions:
    name: principal_motions
    description: Description of principal motions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: principal_motions
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
    multivalued: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    description: A human-readable name or title for this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A detailed textual description of this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string