PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

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


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:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Disulfides / chemistry*
  • Internet
  • Peptides / chemistry*
  • Peptides, Cyclic / chemistry*
  • Protein Conformation
  • Software*


  • Disulfides
  • Peptides
  • Peptides, Cyclic