Biologically important macromolecules made up of long chains of amino acids.

Entity["Protein",name] or

represents an entity of type "Protein".

[prop]

gives the value of a specified property.

[{propi,}]

gives the value of a list of properties.

EntityClass["Protein",{propispeci,}]

represents a class of entities with values of propi defined by speci.

Sample Entities

Sample Entity Classes

Properties

  • AdditionalAtomTypesadditional atom types
    BallAndStickDiagramball and stick diagram
    BiologicalProcessesbiological processes
    CellularComponentscellular components
    ChainLabelschain labels
    DomainIDsdomain IDs
    DomainPositionsdomain positions
    Domainsdomains
    Genegene
    GeneIDgene ID
    GyrationRadiusgyration radius
    Membershipsmemberships
    MolecularFunctionsmolecular functions
    MolecularWeightmolecular weight
    Namename
    NCBIAccessionsNCBI accessions
    PDBIDListPDBID list
    PrimaryPDBIDprimary PDBID
    PrimaryPDBURLprimary PDB URL
    SecondaryStructureRulessecondary structure rules
    Sequencesequence
    SequenceLengthreference sequence length
    SpacefillingDiagramspacefilling diagram
    StructureDiagramribbon diagram
    WireframeDiagramwireframe diagram

Details

  • "Protein" entities each represent a particular known protein.
  • "Protein" entity classes group entities by the biological process they participate in, e.g. "peptidyl-arginine N-methylation", or by the greater structure they belong to, e.g. "cytosolic ribosome" and "outer membrane" and "tRNA-intron endonuclease complex".
  • Some properties are available for the "Protein" entity as a whole and can be given using the form EntityValue["Protein",property]. Such properties include:
  • "Properties"the list of available properties
    "PropertyCanonicalNames"the standard names of available properties
    "SampleEntities"a sample list of available entities (typically of length 10)
    "SampleEntityClasses"a sample list of available entity classes (typically of length 10)
    "EntityCount"number of entities available
    "Entities"the list of available entities
    "EntityCanonicalNames"the standard names of available entities
    "EntityClasses"the list of available entity classes
    "EntityClassCanonicalNames"the standard names of available entity classes
    "PropertyClasses"the list of available property classes
    "PropertyClassCanonicalNames"the standard names of available property classes
    "PropertyCount"number of properties available
  • The following annotations can be used in the third argument of EntityValue["Protein",property,annotation]:
  • "Source"source information for the property
    "Date"the date associated with the entity-property value (if any)
    "EntityAssociation"an association of entities and entity-property values
    "PropertyAssociation"an association of properties and entity-property values
    "EntityPropertyAssociation"an association in which the specified entities are keys, and values are a nested association of properties and entity-property values
    "PropertyEntityAssociation"an association in which the specified properties are keys, and values are a nested association of entities and entity-property values
    "Dataset"a dataset in which the specified entities are keys, and values are an association of property names and entity-property values
  • The following annotations can be used in the second argument of EntityValue[property,annotation]:
  • "Qualifiers"the list of possible qualifiers for the property
    "QualifierValues"the list of possible values that can be given to each qualifier
    "DefaultQualifierValues"the list of default values for the property's qualifiers
    "Description"a brief textual description of the property
    "Definition"a detailed textual definition of the property
    "PhysicalQuantity"the physical quantity associated with the entity-property value
    "Unit"the unit associated with the entity-property value
  • A qualifier value of Automatic indicates that an applicable format of values can be used; e.g. for the "Date" qualifier, this includes a proper date or date span.

Examples

Basic Examples  (4)

Use for entity discovery:

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Find a property value for an entity:

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Retrieve a dataset of all available properties for an entity:

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Identify notable proteins involved in neuron differentiation:

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