The Protein-Protein Interface Database (PPIDB) is a
comprehensive database of protein-protein interfaces extracted from
experimentally determined structures of protein complexes in the
Protein Data Bank (PDB). PPIDB is designed to facilitate the
construction of well-characterized datasets of protein-protein
interface residues for computational analyses. It incorporates three
widely used protein-protein interface residue (IR) definitions and
allows users to specify desired thresholds for each definition. The
three varieties of IR definition currently supported are:
- Reduction of solvent accessible surface area (ASA) upon
complexation
- Distance between alpha carbons
- Minimum distance between any atom of a residue on one chain
and any atom of a residue on another chain
Queries based on protein name, PDB ID, or Gene Ontology (GO)
function and batch retrieval of IRs for a user-supplied list of PDB
IDs are also supported. Tools for filtering datasets on the basis of
amino acid sequence similarity, structural resolution and for
visualizing IRs within the primary amino acid sequence or mapped onto
the 3D structure of proteins are provided. PPIDB is periodically
updated and synchronized with the PDB, and all entries are timestamped
when they are updated or added to the database. This allows authors to
publish the date on which they queried PPIDB, allowing later
comparisons to be made on the exact same dataset.
Additionally, the PPIDB query tools are available as web
services that can be programatically accessed directly by client
programs.
