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Bioinformatics Advance Access published online on June 22, 2007
Bioinformatics, 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 1,3,* and Sanbo Qin 1,2

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

*To whom correspondence should be addressed. Prof. Huan-Xiang Zhou, E-mail: zhou{at}sb.fsu.edu; Phone: (850) 645-1336; fax: (850) 644-7244


  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 underrepresented ones. Future developments will be directed at tackling problems such as building structural models for multi-component structural complexes.

Associate Editor: Dr. Jonathan Wren

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

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