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PEDS Advance Access originally published online on March 24, 2006
Protein Engineering Design and Selection 2006 19(6):265-275; doi:10.1093/protein/gzl009
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues

Usha K. Muppirala1 and Zhijun Li1,2,3

1 Bioinformatics Program, University of the Sciences in Philadelphia Philadelphia, PA 19104, USA 2 Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia Philadelphia, PA 19104, USA

3To whom correspondence should be addressed. E-mail: z.li{at}usip.edu

Evolutionarily conserved hydrophobic residues at the core of protein structures are generally assumed to play a structural role in protein folding and stability. Recent studies have implicated that their importance to protein structures is uneven, with a few of them being crucial and the rest of them being secondary. In this work, we explored the possibility of employing this feature of native structures for discriminating non-native structures from native ones. First, we developed a network tool to quantitatively measure the structural contributions of individual amino acid residues. We systematically applied this method to diverse fold-type sets of native proteins. It was confirmed that this method could grasp the essential structural features of native proteins. Next, we applied it to a number of decoy sets of proteins. The results indicate that such an approach indeed identified non-native structures in most test cases. This finding should be of help for the investigation of the fundamental problem of protein structure prediction.

Keywords: connectivity pattern/conserved hydrophobic residue/hub-residue/network/protein structure

Received October 18, 2005; revised February 1, 2006; accepted February 21, 2006.

Edited by Dek Woolfson


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