Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

Background: Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB). Results: We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set o...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Andrew J. Bordner, Andrey A. Gorin
• Keywords: BMCBI 2008, Protein Complexes, Protein-protein Interactions, X-ray Crystallographic Structures