title: PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
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.
authors.affiliation: INSERM, U973, MTi, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Thévenet
authors.forename: Yimin
authors.initials: Y
authors.lastname: Shen
authors.forename: Julien
authors.initials: J
authors.lastname: Maupetit
authors.forename: Frédéric
authors.initials: F
authors.lastname: Guyon
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.forename: Pierre
authors.initials: P
authors.lastname: Tufféry
mesh_terms: D004220:Disulfides / Q000737:chemistry*; D020407:Internet; D010455:Peptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software
chemical_list: D004220:Disulfides; D010455:Peptides; D010456:Peptides, Cyclic