DPAM

A Domain Parser for Alphafold Models

DPAM: A Domain Parser for AlphaFold Models （https://www.biorxiv.org/content/10.1101/2022.09.22.509116v1, accepted by Protein Science)

Updates:

Upload domain parser results for six model organisms. (2022-12-6)

Replace Dali with Foldseek for initial hits searching. (2022-11-30)

Fix a bug in analyze_PDB.py which prevents the proper usage of Dali results. (2022-10-31)

Prerequisites:

Software and packages

HH-suite3: https://github.com/soedinglab/hh-suite (enable addss.pl to add secondary structure)
DaliLite.v5: http://ekhidna2.biocenter.helsinki.fi/dali/
Python 3.8
Foldseek
mkdssp
pdbx: https://github.com/soedinglab/pdbx
pdb2fasta (https://zhanggroup.org/pdb2fasta)

Please add above software to environment path for DPAM. We also provide a script check_dependencies.py to check if above programs can be found.

Supporting database:

hhsearch UniRef database (https://wwwuser.gwdg.de/~compbiol/uniclust/2022_02/)
pdb70 (https://conglab.swmed.edu/DPAM/pdb70.tgz)
ECOD database
- ECOD ID map to pdb
- ECOD domain length
- ECOD domain list
- ECOD norms
- ECOD domain quality information
- ECOD residue weight in domains
- ECOD70 domain structures
- ECOD70 foldseek database

We provide a script download_all_data.sh that can be used to download all of these databases.

bash download_all_data.sh <DOWNLOAD_DIR>

After downloading the databases, please decompress files. All supporting database files should be put in the same directory and the directory should be provided to DPAM.py as <datadir>. The <datadir> should have the following structure and files.

<datadir>/
    ECOD70/
    ecod_domain_info/
    ECOD_foldseek_DB/
    ecod_weights/
    pdb70/
    UniRef30_2022_02/
    ecod.latest.domains
    ECOD_length
    ECOD_norms
    ECOD_pdbmap

Installation

git clone https://github.com/CongLabCode/DPAM.git

conda install -c qianlabcode dpam

Usage

python DPAM.py <input_cif/pdb> <input_pae> <accession> <output_dir> <threads> <datadir>

Future improvments

Incoperate mmseq to improve search speed
Provide public server and incoperate with ECOD database

EBGU / DPAM