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Bioinformatics Advance Access originally published online on July 23, 2009
Bioinformatics 2009 25(20):2639-2645; doi:10.1093/bioinformatics/btp449
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential

Ami Levy-Moonshine 1,*, El-ad David Amir 1 and Chen Keasar 1,2

1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel

* To whom correspondence should be addressed.


  Abstract

Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models.

Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.

Availability: The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/~meshi.

Contact: chen.keasar{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on March 30, 2009; revised on June 30, 2009; accepted on July 15, 2009

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