shall-we-dance/alphafold-db

Fix Database problem for AlphaFold by updating some databases.

AlphaFold-DB

Update 04/14/23: To Match AlphaFold v2.3.2

Update 03/18/23: To Match AlphaFold v2.3.1

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Fix Database problem for AlphaFold.

While using AlphaFold to make prediction, the pipeline would be failed sometimes, since the databases used to generate the matrix are old, as they used in those papers.

For example: "HHblits fail"

What's different

1. Databases below are updated:

• uniclust30
• mgnify
• pdb70

2. Changed docker/run_docker.py to fetch up the databases' update.

How to use

1. Clone this repository

wget https://github.com/Shall-We-Dance/AlphaFold-DB/archive/refs/tags/v2.3.2.zip
unzip v2.3.2.zip
rm v2.3.2.zip

2. Install

Get the alphafold code.

wget https://github.com/deepmind/alphafold/archive/refs/tags/v2.3.2.zip
unzip v2.3.2.zip
rm v2.3.2.zip

Then, copy the script into it.

cp -r -f <AlphaFold-DB_dir>/* <alphafold_dir>/

Setup the alphafold following the manual provided by alphafold.

3. If you already installed the alphafold

Just redownload the updated databases using script/update.sh.

scripts/update.sh <DOWNLOAD_DIR>

📒 Note: The download directory <DOWNLOAD_DIR> should not be a subdirectory in the AlphaFold repository directory. If it is, the Docker build will be slow as the large databases will be copied during the image creation.

4. The structure of <DOWNLOAD_DIR>

Once the script has finished, you should have the following directory structure:

(This size info is updated at Dec 23, 2021. Size may vary for the latest version.)

$DOWNLOAD_DIR/                             # Total: ~ 2.4 TB (download: ~510 GB)
    bfd/                                   # ~ 1.7 TB (download: 271.6 GB)
        # 6 files.
    mgnify/                                # ~ 64 GB (download: 35 GB)
        mgy_clusters.fa
    params/                                # ~ 3.5 GB (download: 3.5 GB)
        # 5 CASP14 models,
        # 5 pTM models,
        # 5 AlphaFold-Multimer models,
        # LICENSE,
        # = 16 files.
    pdb70/                                 # ~ 65 GB (download: 22 GB)
        # 9 files.
    pdb_mmcif/                             # ~ 206 GB (download: 46 GB)
        mmcif_files/
            # About 180,000 .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/                            # ~ 206 GB (download: 46 GB)
        uniref30_2022_02/
            # 13 files.
    uniprot/                               # ~ 98.3 GB (download: 49 GB)
        uniprot.fasta
    uniref90/                              # ~ 58 GB (download: 29.7 GB)
        uniref90.fasta

Which is different form the original one.

$DOWNLOAD_DIR/                             # 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 180,000 .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
    uniclust30/                            # ~ 86 GB (download: 24.9 GB)
        uniclust30_2018_08/
            # 13 files.
    uniprot/                               # ~ 98.3 GB (download: 49 GB)
        uniprot.fasta
    uniref90/                              # ~ 58 GB (download: 29.7 GB)
        uniref90.fasta