This is distribution for lab members

Not a stand-alone tool. Designed for seoklab cluster3

Setup Requirements:

1. Configure paths in config.py - Update Site2/config.py with your specific paths:

   • SITE_DB_HOME: Path to site database
   • SDF_DB: Path to ligand SDF database
   • RCSB_mmcif_DB: Path to RCSB mmCIF files
   • BABEL: Path to OpenBabel executable
   • mmseqs/foldseek: Tool paths and database paths

2. Dependencies:

   • Galaxy and GalaxyPipe packages
   • OpenBabel
   • pdb files are downloaded on the fly from RCSB PDB database, mmcif is used for info parsing mainly
   • Custom databases: Full mmCIF DB, ligand ideal SDF DB (SDF can be downloaded on the fly as well, but directory should be set in config.py)
   • foldseek and/or mmseqs2 (depending on -tsm option)

How to run ..

$ python3 run_site.py -p {protein PDB file} -tsm foldseek -t result