relational database of structurally defined protein interfaces

View the Project on GitHub fredpdavis/pibase

What is PIBASE?

PIBASE is a comprehensive relational database of all protein structural interfaces extracted from the Protein Data Bank and PISA structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected. A series of properties are then computed for each domain, interface, and complex.

The last release (v2010) uses protein structures from PDB (Sep 2010) and PISA (Sep 2010), domain definitions and classifications from SCOP (v1.75) and CATH (v3.3.0).

NOTE: The PIBASE server at Janelia was retired in August 2015.
The UCSF mirror is still available: http://salilab.org/pibase

The code is maintained here for archiving, and a mysql dump of the database is available at https://zenodo.org/record/29589


Email me at fredpdavis at gmail dot com


If you use the software, database, or webserver, please cite:
PIBASE: a comprehensive database of structurally defined protein interfaces.
Davis FP, Sali A. Bioinformatics (2005) 21(0): 1901-1907.