AlphaFold FUSE filesystem

You are viewing a FUSE (Filesystem in userspace: https://en.wikipedia.org/wiki/Filesystem_in_Userspace) interface for accessing the AlphaFold database. This filesystem is designed to ease access to AlphaFold generated structures, as the 280+ million files would be difficult to organize an operate through on a traditional filesystem. This file describes the basics of using this filesystem, organized by the relative paths inside this file system.

Ultimately, each AlphaFold structure corresponds to a single UniProt record. This tool provides different ways to look up and access those records. Many users will find it quickest to look through the filesystem themselves, but for those who would like to read the full documentation, it is available below. Note that for large folders, it will be much quicker to run ls -f --color=never which will not sort the files or get their attributes, but just print their names.

A few quick notes on data access:

1. For those who intend to read every file in the archive, iterating through the taxonomy ID folder (and subfolders) will be the quickest due to how the AlphaFold source data files are structured. Alternatively, use the Python helper module to access the structure files in the fastest possible manner.
2. For those who want a single structure (or some number of structures) the files can be accessed using a shortcut path, bypassing the sudirectories: /reboxitory/alphafolddb/uniprot/$uniprot_ID_$version.cif where $uniprot_ID is replaced with a UniProt ID, and $version is replaced with a version string. ('v3' or 'v4' at the time this documentation was written.)

List of files and directories in this filesystem

• /reboxitory/alphafolddb/README.md - This file
• /reboxitory/alphafolddb/v3/ OR /reboxitory/alphafolddb/v4/ - The top level directories will indicate which versions of the AlphaFold files are available. If a given file is not available in the requested version, the next highest version of the file will be returned instead. For example, version 4 consists of just 0.5% of the files in version 3. When requesting version 4, if a version 4 file exists it will be returned, and if not version 3 will be returned. On the other hand, v3 will not return v4 files. (If v2 files existed where no v3 file existed it would be returned, but version 3 is the first version available.) In future paths, this part of the path will be referred to as $version.

By PDB

• /reboxitory/alphafolddb/$version/pdb/ - a directory which can be traversed to look up UniProt IDs associated with the PDB ID. You must first go through two subdirectories which correspond to the third from last and second from last character in the PDB ID.
  • /reboxitory/alphafolddb/$version/pdb/2/A/ - a directory which lists all PDB IDs (which have associated UniProt IDs) that have 2A as the second and third from last characters in the PDB ID. For example, this includes the ID 12AS.
    • /reboxitory/alphafolddb/$version/pdb/2/A/12AS - a directory which contains all UniProt IDs associated with the specified PDB ID.
      • /reboxitory/alphafolddb/$version/pdb/2/A/12AS/P00963_v3.cif - an example of a structure file found in the directory above

By taxonomy ID

• /reboxitory/alphafolddb/$version/taxonomy/ - a directory which can be traversed to look up UniProt IDs associated with the given taxonomy ID. You must first go through two subdirectories which correspond to the third from last and second from last character in the taxonomy ID.
  • /reboxitory/alphafolddb/$version/taxonomy/2/3 - a directory which lists all taxonomy IDs (which have associated UniProt IDs) that have 23 as the second and third from last characters in the taxonomy ID. For example, this includes the ID 2206232.
    • /reboxitory/alphafolddb/$version/taxonomy/2/3/2022238 - a directory which contains all UniProt IDs associated with the specified taxonomy ID.
      • /reboxitory/alphafolddb/$version/taxonomy/2/3/2022238/A0A221S5L8_v3.cif - a structure for the taxonomy ID above

By UniProt ID

• /reboxitory/alphafolddb/$version/uniprot/ - a directory which can be traversed to look up UniProt IDs associated with the given UniProt ID substrings. You must first go through two subdirectories which correspond to the third from last and second from last character in the UniProt IDs.
  • /reboxitory/alphafolddb/$version/uniprot/P/F - a directory which lists all UniProt IDs that have PF as the second and third from last characters in the UniProt ID. For example, this includes the ID A0A6I3SPF8.
    • /reboxitory/alphafolddb/$version/uniprot/P/F/A0A6I3SPF8_v3.cif - an example structure file found in the above directory

Shortcut path

• /reboxitory/alphafolddb/$version/uniprot/A0A496APF7 or /reboxitory/alphafolddb/$version/uniprot/A0A496APF7.cif - a direct reference to the structure for a given UniProt ID - no need to go through the subdirectories as shown above.