Current Project

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. Queries based on protein name, PDB ID, or Gene Ontology (GO) function and batch retrieval of IRs for single polypeptide chains, or for pairs of chains are supported. Tools for filtering datasets on the basis of amino acid sequence similarity 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. PPIDB can be accessed through a set of Web services or a Web query interface at http://ppidb.cs.iastate.edu.