PPIRef

PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip TBD

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

How to use

It is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:
from ppiref.utils.misc import download_from_zenodo
download_from_zenodo('ppi_6A.zip')