alphafold3

AlphaFold3 Example

Download databases

The databases for AlphaFOld3 (AF3) must be downloaded. We provide the script we used below. Adjust the DATABASE_DIR as needed.

#!/usr/bin/env bash

## Alphafold 3.0.0 database download
## Pulled from provided fetch_databases.py 
##
## JV Nov 21, 2024
## help@sbgrid.org

# get zstd in path
export PATH=$PATH:$HOME/.local/bin

files=(
 'bfd-first_non_consensus_sequences.fasta.zst'
 'mgy_clusters_2022_05.fa.zst'
 'nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst'
 'pdb_2022_09_28_mmcif_files.tar.zst'
 'pdb_seqres_2022_09_28.fasta.zst'
 'rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst'
 'rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst'
 'uniprot_all_2021_04.fa.zst'
 'uniref90_2022_05.fa.zst'
)

DATABASE_DIR="/programs/local/alphafold-3.0.0/databases"
GOOGLE_URL="https://storage.googleapis.com/alphafold-databases/v3.0"

for filename in "${files[@]}"; do
  echo "Fetching: $filename"
  echo "curl --progress-bar --continue-at - --output ${DATABASE_DIR}/${filename} ${GOOGLE_URL}/${filename} "
done

for filename in "${files[@]}"; do
  echo "Uncompressing: $filename"
  echo "zstd --decompress --force ${DATABASE_DIR}/${filename}"
done

The resulting layout:

/programs//local/alphafold-3.0.0/databases/
├── bfd-first_non_consensus_sequences.fasta
├── compressed
│   ├── bfd-first_non_consensus_sequences.fasta.zst
│   ├── mgy_clusters_2022_05.fa.zst
│   ├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst
│   ├── pdb_2022_09_28_mmcif_files.tar.zst
│   ├── pdb_seqres_2022_09_28.fasta.zst
│   ├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst
│   ├── rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst
│   ├── uniprot_all_2021_04.fa.zst
│   └── uniref90_2022_05.fa.zst
├── mgy_clusters_2022_05.fa
├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta
├── pdb_2022_09_28_mmcif_files.tar
├── pdb_seqres_2022_09_28.fasta
├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta
├── rnacentral_active_seq_id_90_cov_80_linclust.fasta
├── uniprot_all_2021_04.fa
└── uniref90_2022_05.fa