fetch_alphafold_aligned_error: Fetch AlphaFold aligned error

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Fetch AlphaFold aligned error

Description

Fetches the aligned error for AlphaFold predictions for provided proteins. The aligned error is useful for assessing inter-domain accuracy. In detail it represents the expected position error at residue x (scored residue), when the predicted and true structures are aligned on residue y (aligned residue).

Usage

fetch_alphafold_aligned_error(
  uniprot_ids = NULL,
  error_cutoff = 20,
  timeout = 30,
  max_tries = 1,
  version = "v6",
  return_data_frame = FALSE,
  show_progress = TRUE
)

Arguments

uniprot_ids	a character vector of UniProt identifiers for which predictions should be fetched.
error_cutoff	a numeric value specifying the maximum position error (in Angstroms) that should be retained. setting this value to a low number reduces the size of the retrieved data. Default is 20.
timeout	a numeric value specifying the time in seconds until the download times out. The default is 30 seconds.
max_tries	a numeric value that specifies the number of times the function tries to download the data in case an error occurs. The default is 1.
version	a character value that specifies the alphafold version that should be used. This is regularly updated by the database. We always try to make the current version the default version. Available version can be found here: https://ftp.ebi.ac.uk/pub/databases/alphafold/
return_data_frame	a logical value; if TRUE a data frame instead of a list is returned. It is recommended to only use this if information for few proteins is retrieved. Default is FALSE.
show_progress	a logical value; if TRUE a progress bar will be shown. Default is TRUE.

Value

A list that contains aligned errors 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:

• scored_residue: The error for this position is calculated based on the alignment to the aligned residue.

• aligned_residue: The residue that is aligned for the calculation of the error of the scored residue

• error: The predicted aligned error computed by alpha fold.

• accession: The UniProt protein identifier.

Examples

aligned_error <- fetch_alphafold_aligned_error(
  uniprot_ids = c("F4HVG8", "O15552"),
  error_cutoff = 5,
  return_data_frame = TRUE
)

head(aligned_error, n = 10)

protti documentation built on Jan. 14, 2026, 9:08 a.m.