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"EncyclopediaOfDomains" (Service Connection)

Connect to the The Encyclopedia of Domains using the Wolfram Language to get information about protein domains in the AlphaFold protein structure database.

Connecting & Authenticating

ServiceConnect["EncyclopediaOfDomains"] creates a connection to the The Encyclopedia of Domains.

Requests

ServiceExecute["EncyclopediaOfDomains","request",params] sends a request to The Encyclopedia of Domains Database API, using parameters params. The following give possible requests.

Details about Domains

"Domains" — get details about all the domains in a protein as a Tabular object

Parameters:
  • "UniProtID"NoneUniProt ID

    • Summary Information Related to the Organism

    "OrganismSummary" — get summary information about the organism whose domains you are interested in as a Dataset

    Parameters:
  • "UniProtID"NoneUniProt ID

    • BioMolecule Structures

    "BioMolecule" — get BioMolecule structure of a protein domain

    Parameters:
  • "DomainID"NoneDomain ID

    • "DomainStructures" — get the biomolecular structures of all domains in a protein

    Parameters:
  • "UniProtID"NoneUniProt ID

    • Parsed domains

    "ParsedDomains" — get the detailed information about domains parsed by different methods to reach to a consensus parse as a Tabular object; methods include: Merizo, Chainsaw and UniDoc

    Parameters:
  • "UniProtID"NoneUniProt ID

    • Interaction between domains

    "DomainInteractions" — get information about interaction between domains as a list of {domi, domj, paeij}

    Parameters:
  • "UniProtID"NoneUniProt ID

    • Two domains (domi, domj) interact with each other if there are at least three interdomain CB atom pairs within 8 angstroms of each other. A median interdomain PAE (Predicted Aligned Error, paeij) less than 4 angstroms indicates high confidence in the domain interactions.

    Examples

    open all close all

    Basic Examples  (3)

    Create a new connection to the The Encyclopedia of Domains Database:

    Wolfram Language code: encyclopedia = ServiceConnect["EncyclopediaOfDomains"]

    Get information about all the domains in a protein in the AlphaFold protein structure database:

    Wolfram Language code: ServiceExecute[encyclopedia, "Domains", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q13393"]|>]

    Get information about the organism whose domains you are studying:

    Wolfram Language code: ServiceExecute["EncyclopediaOfDomains", "OrganismSummary", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q13393"]|>]

    Get the BioMolecule corresponding to a protein domain:

    Wolfram Language code: bm = ServiceExecute["EncyclopediaOfDomains", "BioMolecule", <|"DomainID" -> "AF-Q13393-F1-model_v4_TED01"|>]

    Visualize the domain structure:

    Wolfram Language code: BioMoleculePlot3D@bm

    Scope  (2)

    Get the biomolecular structures for all protein domains:

    Wolfram Language code: domainStructures = ServiceExecute["EncyclopediaOfDomains", "DomainStructures", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q13393"]|>]

    Visualize the structures:

    Wolfram Language code: BioMoleculePlot3D /@ domainStructures

    Get the detailed information about domains parsed by different methods:

    Wolfram Language code: ServiceExecute["EncyclopediaOfDomains", "ParsedDomains", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q13393"]|>]

    Get information about interdomain interactions:

    Wolfram Language code: ServiceExecute["EncyclopediaOfDomains", "DomainInteractions", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "O14578"]|>]

    Neat Examples  (1)

    Function to visualize domains in a protein:

    Wolfram Language code: domainPlot[id_] := Module[{domains, biomolecule, cathIDs, seqRanges, ranges, colors, colRules}, domains = ServiceExecute["EncyclopediaOfDomains", "Domains", {"UniProtID" -> id}]; biomolecule = ServiceExecute["AlphaFoldDatabase", "BioMolecule", <|"UniProtID" -> id|>]; cathIDs = Normal@domains[[All, 2]];seqRanges = Normal@domains[[All, 4]]; ranges = Flatten@MapApply[Range, #]& /@ seqRanges; colors = ColorData["DefaultPlotColors"][#]& /@ Range@Length@ranges; colRules = Join[Flatten@Table[Table[{"A", j} -> colors[[i]], {j, ranges[[i]]}], {i, Length@ranges}], {_ -> StandardGray}]; Legended[BioMoleculePlot3D[biomolecule, ColorRules -> colRules], SwatchLegend[colors, cathIDs, LegendMarkers -> "Bubble"]]]

    Visualize the domains in the protein supervillin, which links the actin cytoskeleton to the membrane and is involved in various biological functions like costamere assembly during myogenesis, myosin II assembly and regulation, early cell spreading during migration and invadopodial function:

    Wolfram Language code: domainPlot[ExternalIdentifier["UniProtKBAccessionNumber", "O95425"]]