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

Abstract

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.

Authors:
 [1];  [2]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mayo Clinic, Scottsdale, AZ (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1263826
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
BMC Bioinformatics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1471-2105
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bordner, Andrew J., and Gorin, Andrey A. Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. United States: N. p., 2008. Web. doi:10.1186/1471-2105-9-234.
Bordner, Andrew J., & Gorin, Andrey A. Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. United States. doi:10.1186/1471-2105-9-234.
Bordner, Andrew J., and Gorin, Andrey A. Mon . "Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces". United States. doi:10.1186/1471-2105-9-234. https://www.osti.gov/servlets/purl/1263826.
@article{osti_1263826,
title = {Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces},
author = {Bordner, Andrew J. and Gorin, Andrey A.},
abstractNote = {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.},
doi = {10.1186/1471-2105-9-234},
journal = {BMC Bioinformatics},
number = 1,
volume = 9,
place = {United States},
year = {2008},
month = {5}
}

Journal Article:
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Cited by: 24 works
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