baba-hashimoto / dpam

A domain parser for Alphafold models

DPAM

A domain parser for Alphafold models

Prerequisites:

Software

• 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.

Database:

• hhsearch UniRef database (https://wwwuser.gwdg.de/~compbiol/uniclust/2022_02/)
• pdb70 (https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)
• ECOD database

Other auxiliary data required for the software:

• 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

Installation

After installing required software and downloading the DPAM and necessary auxiliary data, please modify the config_file so DPAM can access the required data.

Usage

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]

Future improvments

• Incoperate mmseq and foldseek to accelerate speed of the search
• Provide server for public usage and integrate with ECOD