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. 2012 Jul;40(Web Server issue):W288-93.
doi: 10.1093/nar/gks419. Epub 2012 May 11.

PEP-FOLD: An Updated De Novo Structure Prediction Server for Both Linear and Disulfide Bonded Cyclic Peptides

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Free PMC article

PEP-FOLD: An Updated De Novo Structure Prediction Server for Both Linear and Disulfide Bonded Cyclic Peptides

Pierre Thévenet et al. Nucleic Acids Res. .
Free PMC article

Abstract

In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution. We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids. The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists. Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 Å from the full NMR structures. Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 Å RMS from the NMR rigid cores. The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server. The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD.

Figures

Figure 1.
Figure 1.
PEP-FOLD 2012 flowchart.
Figure 2.
Figure 2.
PEP-FOLD models. The experimental conformation is in green. PEP-FOLD models are in cyan. From left to right, top to bottom: 1e0n (A), 1psv (B), 2l0g (C), 1n0a (D), 2ki0 (E), 1kwd (F) and 2gdl (G) lowest-energy models and 1wm8 (H) best model.

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