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

Bordner, Andrew J.; Gorin, Andrey A.

doi:10.1186/1471-2105-9-234

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

Journal Article · Mon May 12 00:00:00 EDT 2008 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-9-234· OSTI ID:1263826

Bordner, Andrew J. ^[1]; Gorin, Andrey A. ^[2]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mayo Clinic, Scottsdale, AZ (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Here, protein-protein interactions are ubiquitous and essential for cellular processes. High-resolution X-ray crystallographic structures of protein complexes can elucidate the details of their function and provide a basis for many computational and experimental approaches. Here we demonstrate that existing annotations of protein complexes, including those provided by the Protein Data Bank (PDB) itself, contain a significant fraction of incorrect annotations. 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 of properties; and (4) finally combining these scores for each entry in order to predict the complex structure. Unlike previous annotation methods, consistent prediction of complexes with identical or almost identical protein content is insured. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1263826

Journal Information:: BMC Bioinformatics, Vol. 9, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 26 works

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