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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(17):2203-2209; doi:10.1093/bioinformatics/btm323
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Interaction-site prediction for protein complexes: a critical assessment

Huan-Xiang Zhou 1,2,3,* and Sanbo Qin 1,2

1Institute of Molecular Biophysics, 2School of Computational Science and 3Department of Physics, Florida State University, Tallahassee, Florida 32306, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Proteins function through interactions with other proteins and biomolecules. Protein–protein interfaces hold key information toward molecular understanding of protein function. In the past few years, there have been intensive efforts in developing methods for predicting protein interface residues. A review that presents the current status of interface prediction and an overview of its applications and project future developments is in order.

Summary: Interface prediction methods rely on a wide range of sequence, structural and physical attributes that distinguish interface residues from non-interface surface residues. The input data are manipulated into either a numerical value or a probability representing the potential for a residue to be inside a protein interface. Predictions are now satisfactory for complex-forming proteins that are well represented in the Protein Data Bank, but less so for under-represented ones. Future developments will be directed at tackling problems such as building structural models for multi-component structural complexes.

Contact: zhou{at}sb.fsu.edu

Associate Editor: Jonathan Wren

Received on May 21, 2007; revised on June 11, 2007; accepted on June 11, 2007

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S. Qin and H.-X. Zhou
meta-PPISP: a meta web server for protein-protein interaction site prediction
Bioinformatics, December 15, 2007; 23(24): 3386 - 3387.
[Abstract] [Full Text] [PDF]


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