A domain parser for Alphafold models
- 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
- pdbx: https://github.com/soedinglab/pdbx
Above software is required to be added to $PATH for smooth execution of the DPAM.
- hhsearch UniRef database (https://wwwuser.gwdg.de/~compbiol/uniclust/2022_02/)
- pdb70 (https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)
- ECOD database
- ECOD map to pdb
- ECOD domain length
- ECOD domain list (need to decompress)
- ECOD norms
- ECOD domain info (https://conglab.swmed.edu/DPAM/)
- ECOD residue weight (https://conglab.swmed.edu/DPAM/)
- ECOD database (https://conglab.swmed.edu/DPAM/)
Please put the first four files in the same directory as scripts, decompress ECOD domain quality, ECOD residue weight and ECOD database and indicate their locations in the config_file
After installing required software and downloading the DPAM and necessary auxiliary data, please modify the config_file so DPAM can access the required data.
Currently DPAM works on AlphaFold v2 json file and please put json file and model file at the same direstory.
DPAM.py [model name.cif] [output_dir]
- Incoperate mmseq and foldseek to accelerate speed of the search
- Provide server for public usage and integrate with ECOD