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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W498-503. doi: 10.1093/nar/gkp323. Epub 2009 May 11.

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

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MTi, INSERM UMR-S 973, - Paris 7, 35 rue H. Brion, F75205, Paris, France.


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 A Calpha root mean square deviation from the full NMR structures. PEP-FOLD can be accessed at

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