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Nucleic Acids Research Advance Access originally published online on May 11, 2009
Nucleic Acids Research 2009 37(Web Server issue):W498-W503; doi:10.1093/nar/gkp323
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W498-W503
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PEP-FOLD: an online resource for de novo peptide structure prediction

Julien Maupetit1,2, Philippe Derreumaux3 and Pierre Tuffery1,2,*

1MTi, INSERM UMR-S 973, - Paris 7, 35 rue H. Brion, F75205, Paris, 2RPBS, Université Paris Diderot - Paris 7, 35 rue H. Brion, F75205, Paris and 3Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F75005, Paris, France

*To whom correspondence should be addressed. Tel: +331 5727 8374; Fax: +331 5727 8372; Email: pierre.tuffery{at}univ-paris-diderot.fr

Received January 30, 2009. Revised April 5, 2009. Accepted April 20, 2009.

Rational peptide design and large-scale prediction of peptide structure from sequence remain a challenge for chemical biologists. We present PEP-FOLD, an online service, aimed at de novo modelling of 3D conformations for peptides between 9 and 25 amino acids in aqueous solution. Using a hidden Markov model-derived structural alphabet (SA) of 27 four-residue letters, PEP-FOLD first predicts the SA letter profiles from the amino acid sequence and then assembles the predicted fragments by a greedy procedure driven by a modified version of the OPEP coarse-grained force field. Starting from an amino acid sequence, PEP-FOLD performs series of 50 simulations and returns the most representative conformations identified in terms of energy and population. Using a benchmark of 25 peptides with 9–23 amino acids, and considering the reproducibility of the runs, we find that, on average, PEP-FOLD locates lowest energy conformations differing by 2.6 Å C{alpha} root mean square deviation from the full NMR structures. PEP-FOLD can be accessed at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD


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