Skip to content

Alphafold Databases

Jump to bottom
amrismil edited this page Oct 28, 2025 · 3 revisions

For the standard MSA and features calculation, AlphaPulldown requires genetic databases. Check if you have downloaded the necessary parameters and databases (e.g., BFD, MGnify, etc.) as instructed in AlphaFold's documentation. You should have a directory for databases structured as follows:

alphafold_database/                             # Total: ~ 2.2 TB (download: 438 GB)
   bfd/                                   # ~ 1.7 TB (download: 271.6 GB)
       # 6 files.
   mgnify/                                # ~ 64 GB (download: 32.9 GB)
       mgy_clusters_2018_12.fa
   params/                                # ~ 3.5 GB (download: 3.5 GB)
       # 5 CASP14 models,
       # 5 pTM models,
       # 5 AlphaFold-Multimer models,
       # LICENSE,
       # = 16 files.
   pdb70/                                 # ~ 56 GB (download: 19.5 GB)
       # 9 files.
   pdb_mmcif/                             # ~ 206 GB (download: 46 GB)
       mmcif_files/
           # About 227,000 .cif files.
       obsolete.dat
   pdb_seqres/                            # ~ 0.2 GB (download: 0.2 GB)
       pdb_seqres.txt
   small_bfd/                             # ~ 17 GB (download: 9.6 GB)
       bfd-first_non_consensus_sequences.fasta
   uniref30/                            # ~ 86 GB (download: 24.9 GB)
           # 14 files.
   uniprot/                               # ~ 98.3 GB (download: 49 GB)
       uniprot.fasta
   uniref90/                              # ~ 58 GB (download: 29.7 GB)
       uniref90.fasta

Note

Uniclust30 is the version of the database generated before 2019, UniRef30 is the one generated after 2019. Please note that AlphaPulldown is using UniRef30_2023_02 by default. This version can be downloaded by this script. Alternatively, please overwrite the default path to the uniref30 database using the --uniref30_database_path flag of create_individual_features.py.

Note

Since the local installation of all genetic databases is space-consuming, you can alternatively use the remotely-run MMseqs2 and ColabFold databases. Follow the corresponding instructions. However, for AlphaPulldown to function, you must download the parameters stored in the params/ directory of the AlphaFold database by downloading and executing this script: https://github.com/google-deepmind/alphafold/blob/main/scripts/download_alphafold_params.sh



Clone this wiki locally