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Open Access Methodology article

Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials

Karin Noy1*, Nir Kalisman2 and Chen Keasar12

Author Affiliations

1 Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel

2 Department of Computer Sciences, Ben-Gurion University, Beer-Sheva, Israel

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BMC Structural Biology 2008, 8:27  doi:10.1186/1472-6807-8-27

Published: 29 May 2008

Abstract

Background

The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution.

Results

We tested the new approach on four families of short β-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82).

Conclusion

Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries.