Fetches atom level data for AlphaFold predictions either for selected proteins or whole organisms.
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optional, a character vector of UniProt identifiers for which predictions
should be fetched. This argument is mutually exclusive to the
optional, a character value providing the name of an organism for which
all available AlphaFold predictions should be retreived. The name should be the capitalised
scientific species name (e.g. "Homo sapiens"). Note: Some organisms contain a lot of
predictions which might take a considerable amount of time and memory to fetch. Therefore, you
should be sure that your system can handle fetching predictions for these organisms. This
argument is mutually exclusive to the
a numeric value specifying the time in seconds until the download of an organism archive times out. The default is 3600 seconds.
a logical value that specifies if true, a data frame instead of a list is returned. It is recommended to only use this if not many pdb structures are retrieved. Default is FALSE.
a logical value that specifies if true, a progress bar will be shown. Default is TRUE.
A list that contains atom level data for AlphaFold predictions. If return_data_frame is TRUE, a data frame with this information is returned instead. The data frame contains the following columns:
label_id: Uniquely identifies every atom in the prediction following the standardised convention for mmCIF files.
type_symbol: The code used to identify the atom species representing this atom type. This code is the element symbol.
label_atom_id: Uniquely identifies every atom for the given residue following the standardised convention for mmCIF files.
label_comp_id: A chemical identifier for the residue. This is the three- letter code for the amino acid.
label_asym_id: Chain identifier following the standardised convention for mmCIF files. Since every prediction only contains one protein this is always "A".
label_seq_id: Uniquely and sequentially identifies residues for each protein. The numbering corresponds to the UniProt amino acid positions.
x: The x coordinate of the atom.
y: The y coordinate of the atom.
z: The z coordinate of the atom.
prediction_score: Contains the prediction score for each residue.
auth_seq_id: Same as
auth_comp_id: Same as
auth_asym_id: Same as
uniprot_id: The UniProt identifier of the predicted protein.
score_quality: Score annotations.
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