Prediction of peptide structure: How far are we?
Article first published online: 3 OCT 2006
Copyright © 2006 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 65, Issue 4, pages 889–897, 1 December 2006
How to Cite
Thomas, A., Deshayes, S., Decaffmeyer, M., Van Eyck, M. H., Charloteaux, B. and Brasseur, R. (2006), Prediction of peptide structure: How far are we?. Proteins, 65: 889–897. doi: 10.1002/prot.21151
- Issue published online: 14 NOV 2006
- Article first published online: 3 OCT 2006
- Manuscript Accepted: 3 JUL 2006
- Manuscript Revised: 12 MAY 2006
- Manuscript Received: 7 FEB 2006
- Interuniversity Poles of Attraction Programme—Belgian State, Prime Minister's Office—Federal Office for Scientific, Technical and Cultural Affairs (PAI). Grant Number: P5/33
- Ministère de la Région Wallonne. Grant Numbers: 14540 (PROTMEM), 215140 (αBUSTEC)
- FNRS. Grant Number: 3.4546.02
- structural prediction;
- NMR structures;
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. Proteins 2006. © 2006 Wiley-Liss, Inc.