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"AlphaFoldDatabase" (Service Connection)

Connect to the AlphaFold Protein Structure Database API using the Wolfram Language to get information about protein structures predicted by AlphaFold.

Connecting & Authenticating

ServiceConnect["AlphaFoldDatabase"] creates a connection to the AlphaFold Protein Structure Database API. If a previously saved connection can be found, it will be used; otherwise, a new authentication request will be launched.

Requests

ServiceExecute["AlphaFoldDatabase","request",params] sends a request to the AlphaFold Protein Structure Database API, using parameters params. The following give possible requests.

BioMolecule Structure Details

"PredictedStructureDetails" — get information about a biomolecule structure from the AlphaFold Protein Structure Database

Parameters:
  • "UniProtID"NoneUniProt ID

    • BioMolecule Structure Summary

    "StructureSummary" — get summary about a biomolecule structure from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID

    • BioMolecule Structures

    "BioMolecule" — get a BioMolecule structure from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID
    "IncludeIsoforms"Falseinclude data about isoforms

    • Biomolecular Sequences

    "BioSequence" — get the BioSequence of a BioMolecule from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID
    "IncludeIsoforms"Falseinclude data about isoforms

    • pLDDT Score

    "PredictedLocalDistanceDifferenceTest" — get the pLDDT score of a BioMolecule structure from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID
    "IncludeIsoforms"Falseinclude data about isoforms

    • Predicted Aligned Error

    "PredictedAlignedErrorData" — get the Predicted Aligned Error score of a BioMolecule structure from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID
    "IncludeIsoforms"Falseinclude data about isoforms

    • AlphaMissense Pathogenicity

    "AlphaMissensePathogenicity" — get information about predicted pathogenicity due to point mutations of a BioMolecule structure from the AlphaFold Protein Structure Database

    Parameters:
  • "UniProtID"NoneUniProt ID
    "DatasetScope""AllAminoAcidSubstitutions"dataset type for pathogenicity scores

    • Parameter Details

    Possible values for "DatasetScope" in the request "AlphaMissensePathogenicity" include:
  • "AllAminoAcidSubstitutions"all possible amino acid substitutions
    "HG19"GRCh37 build of the human genome
    "HG38"GRCh38 build of the human genome
    • Possible values for the "IncludeIsoforms" parameter can be True or False to get information about all isoforms or only a single structure, respectively.

    Examples

    open all close all

    Basic Examples  (2)

    Create a new connection to the AlphaFold database:

    Wolfram Language code: alphafold = ServiceConnect["AlphaFoldDatabase"]

    Get the BioMolecule of a predicted structure:

    Wolfram Language code: alphafold["BioMolecule", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"]|>]

    Visualize the structure:

    Wolfram Language code: BioMoleculePlot3D@%

    Get details about a predicted structure by using the UniProt ID:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "PredictedStructureDetails", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P05193"]|>]

    Scope  (6)

    Get the predicted structures of all isoforms of a single canonical protein sequence using the parameter "IncludeIsoforms":

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "BioMolecule", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"], "IncludeIsoforms" -> True|>]

    Visualize the structures:

    Wolfram Language code: BioMoleculePlot3D /@ %

    Get the biomolecular sequences of a protein:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "BioSequence", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"]|>]

    Obtain the sequence of all isoforms using the "IncludeIsoforms" parameter:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "BioSequence", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"], "IncludeIsoforms" -> True|>]

    Get the detailed summary of a predicted structure:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "StructureSummary", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P05193"]|>]

    Get the Predicted Local Distance Difference Test (pLDDT) of a protein:

    Wolfram Language code: (pLDDT = ServiceExecute["AlphaFoldDatabase", "PredictedLocalDistanceDifferenceTest", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"]|>])//Short

    Visualize the pLDDT:

    Wolfram Language code: ListLinePlot[pLDDT, AxesLabel -> {"Residue ID", "pLDDT"}, ImageSize -> Medium]

    Obtain the pLDDT of all isoforms using the "IncludeIsoforms" parameter:

    Wolfram Language code: ListLinePlot /@ ServiceExecute["AlphaFoldDatabase", "PredictedLocalDistanceDifferenceTest", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"], "IncludeIsoforms" -> True|>]

    Get the Predicted Aligned Error (PAE) data of a structure:

    Wolfram Language code: pae = ServiceExecute["AlphaFoldDatabase", "PredictedAlignedErrorData", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"]|>]

    Visualize the PAE, showing regions of high and low relative confidence between pairs of residues:

    Wolfram Language code: MatrixPlot[pae, PlotLegends -> Automatic]

    Obtain the PAE of all isoforms:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "PredictedAlignedErrorData", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"], "IncludeIsoforms" -> True|>]
    Wolfram Language code: MatrixPlot[#, PlotLegends -> Automatic]& /@ %

    Get the full AlphaMissense pathogenicity data for all possible single amino acid mutations. These are the predicted pathogenicity scores and statuses due to point mutations in proteins:

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "AlphaMissensePathogenicity", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P01116"]|>]

    Obtain the pathogenicity scores of all possible single nucleotide missense variants for canonical human proteins for human genome builds GRCh37 ("HG19") and GRCh38 ("HG38"):

    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "AlphaMissensePathogenicity", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P01116"], "DatasetScope" -> "HG19"|>]
    Wolfram Language code: ServiceExecute["AlphaFoldDatabase", "AlphaMissensePathogenicity", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P01116"], "DatasetScope" -> "HG38"|>]

    Neat Examples  (1)

    Visualize the structure with residues color coded by pLDDT:

    Wolfram Language code: Options[pLDDTPlot3D] = {ColorFunction -> "LightTemperatureMap"}; pLDDTPlot3D[uniprotID_, OptionsPattern[]] := Module[ {bm, plddt, chain, cFunc, colorRules}, bm = ServiceExecute["AlphaFoldDatabase", "BioMolecule", <|"UniProtID" -> uniprotID|>]; plddt = ServiceExecute["AlphaFoldDatabase", "PredictedLocalDistanceDifferenceTest", <|"UniProtID" -> uniprotID|>]; cFunc = ColorData[{OptionValue@ColorFunction, {0, 100}}]; chain = First[bm["ChainLabels"]]; colorRules = Thread[Rule[Thread[{chain, Range@Length@plddt}], Map[cFunc, plddt]]]; BioMoleculePlot3D[bm, ColorRules -> colorRules, PlotLegends -> BarLegend[{cFunc, {0, 100}}]]]
    Wolfram Language code: pLDDTPlot3D[ExternalIdentifier["UniProtKBAccessionNumber", "Q5VSL9"]]