AlphaFold is a deep learning tool for predicting a protein’s 3D structure from its amino acid sequence. It was developed by DeepMind and utilizes GPU compute. For more information, see the tool's homepage and GitHub repo.
toolchest.alphafold( inputs, output_path=None, model_preset=None, max_template_date=None, use_reduced_dbs=False, is_prokaryote_list=None, is_async=False, )
toolchest$alphafold( inputs, output_path = NULL, model_preset = NULL, max_template_date = NULL, use_reduced_dbs = FALSE, is_prokaryote_list = NULL, is_async = FALSE )
See the Notes section below for more details.
Use in place of:
Path or list of paths to file(s) that will be passed in as input. A path can be a local filepath or an AWS S3 URI.
(optional) Path to a local directory where the output files will be downloaded.
(optional) Specific AlphaFold model to use. Options are [
(optional) String of date in YYYY-MM-DD format. Restricts protein structure prediction to those in the database before this date. Defaults to today's date.
(optional) Whether to use a smaller version of the BFD database. If true, reduces run time at the cost of result quality.
(optional) List of booleans that determines whether all input sequences in the given FASTA file are prokaryotic. Expects the string normally used input into AlphaFold (e.g. "true,true" if there are two prokaryote inputs).
Whether to run a job asynchronously.
This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.
Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.
is_async parameter to true if you would like to run a AlphaFold job asynchronously. See Async Runs for more information.
Toolchest currently supports version 2.1.2 of AlphaFold. Every request to run AlphaFold with Toolchest will default to this version.
Toolchest's implementation of AlphaFold uses AlphaFold's required genetic sequence databases. For a complete list of databases used, see the tool's GitHub page.
Toolchest supports the following arguments for AlphaFold:
However, these should be specified via specific argument values in the function call, rather than through a generic
tool_args argument (like other Toolchest tools). See Function Arguments for more details.
Updated 27 days ago