PIBASE.ligands: Overlapping small molecule and protein binding sites
What is PIBASE.ligands?
PIBASE.ligands is a resource for analyzing the spatial overlap of protein-protein and protein-ligand interfaces on protein structures. It combines binding site information from PIBASE and LIGBASE with SCOP-based ASTRAL alignments of protein domain families. The database schema is available here. PIBASE is developed at http://pibase.janelia.org, with a mirror maintained at http://salilab.org/pibase.
This web interface enables integrated queries of protein interfaces (domain-domain and domain-peptide), ligand binding sites, and their overlap. More sophisticated searches can be done by downloading the database and querying it locally with MySQL.
The goal of this interface is to allow identification of ligand binding sites that overlap with a protein interface upon alignment. In addition to the domain-domain interfaces stored in PIBASE, the PIBASE.ligands exentesion also stores domain-peptide interfaces and domain-ligand interfaces. Once you have found a protein interface of interest, you can query the database to identify ligand binding sites that overlap after alignment; Or vice versa, once you find a ligand binding site of interest, you can query the database for protein interfaces that overlap with the binding site upon alignment. The overlap can be visualized by sequence alignment or in three-dimensions using a RasMol script (see below).
Rasmol scripts are provided for viewing the interfaces and their overlaps. 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 overlap of small molecule and protein binding sites within families of protein structures.
Davis FP, Sali A. PLoS Comput Biology 2010 6(2): e1000668.
The original PIBASE database is described here: