title: Prediction of peptide structure: how far are we?
abstract: Rational design of peptides is a challenge, which would benefit from a better knowledge of the rules of sequence-structure-function relationships. Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. Structures can also be calculated in silico from primary sequence information using three algorithms: Pepstr, Robetta, and PepLook. The most recent algorithm, PepLook introduces indexes for evaluating structural polymorphism and stability. For peptides with converging experimental data, calculated structures from PepLook and, to a lesser extent from Pepstr, are close to NMR models. The PepLook index for polymorphism is low and the index for stability points out possible binding sites. For peptides with divergent experimental data, calculated and NMR structures can be similar or, can be different. These differences are apparently due to polymorphism and to different conditions of structure assays and calculations. The PepLook index for polymorphism maps the fragments encoding disorder. This should provide new means for the rational design of peptides.
authors.affiliation: Centre de Biophysique Moléculaire Numérique FSAGx, 2, Passage des Déportés, Gembloux 5030, Belgium. thomas.a@fsagx.ac.be
authors.forename: Annick
authors.initials: A
authors.lastname: Thomas
authors.forename: Sébastien
authors.initials: S
authors.lastname: Deshayes
authors.forename: Marc
authors.initials: M
authors.lastname: Decaffmeyer
authors.forename: Marie Hélène
authors.initials: MH
authors.lastname: Van Eyck
authors.forename: Benoit
authors.initials: B
authors.lastname: Charloteaux
authors.forename: Robert
authors.initials: R
authors.lastname: Brasseur
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides