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What is PIBASE?
PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS 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 database schema is available here. PIBASE is developed at http://fredpdavis.com/pibase/, with a mirror maintained at https://salilab.org/pibase.

Note that PIBASE is no longer updated.

Data Sources

data type
March 2008
protein structures
March 2008
predicted quaternary protein structures
domain definitions, classification
domain definitions, classification

Searching PIBASE
This web interface provides basic search functionality for the database - allowing complex-, interface-, and domain- centric searches. More sophisticated searches can be done by installing a local version of the database and querying it via mysql or the provided perl interface.

Viewing structures in PIBASE
Rasmol scripts are provided for viewing the individual interfaces. This script can be used as a rasmol script viewer (in UNIX). The rasmol scripts may also be run on windows machines using "raswin.exe -script scriptname". For help on setting up rasmol as a browser helper please follow this external link.

The interfaces stored in PIBASE have been used to predict protein-protein interactions both within species (S cerevisiae, available at MODBASE; Davis, et al. Nucleic Acids Res 2006) and between species (human and 10 pathogens, available here; Davis, et al. Protein Sci. 2007).

External Software


PIBASE: a comprehensive database of structurally defined protein interfaces. Davis FP, Sali A. Bioinformatics (2005) 21(0): 1901-1907.link. Supplementary Information.

fredpdavis at gmail dot com