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AlphaFold2 Databases

AlphaFold databases are stored in /opt/nesi/db/alphafold_db/ parent directory. In order to make the database calling more convenient, we have prepared modules for each version of the database. Running module spider AlphaFold2DB will list the available versions named after the downladed Year and Month (Year-Month)

terminal

$ module spider AlphaFold2DB

---------------------------------------------
  AlphaFold2DB:
---------------------------------------------
    Description:
      AlphaFold2 databases

     Versions:
        AlphaFold2DB/2022-06
        AlphaFold2DB/2023-04

Loading a module will set the $AF2DB environment variable which is pointing to the selected version of the database. For an example.

terminal

$ module load AlphaFold2DB/2023-04

$ echo $AF2DB 
/opt/nesi/db/alphafold_db/2023-04

Databases and their sizes (T = TB , G = GB , M = MB)

2023-04/
├── bfd               1.8 T
├── mgnify            120 G
├── params            5.3 G
├── pdb70             56G G
├── pdb_mmcif         272 G
│   └── mmcif_files
├── pdb_seqres        480 M
├── small_bfd          17 G
├── uniprot           111 G
├── uniref30          206 G
└── uniref90           73 G
  • Size of 2023-04 database is ~ 2.6 T