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