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Prediction of peptide structure: How far are we?
Author(s) -
Thomas Annick,
Deshayes Sébastien,
Decaffmeyer Marc,
Van Eyck Marie Hélène,
Charloteaux Benoit,
Brasseur Robert
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21151
Subject(s) - peptide , in silico , computational biology , polymorphism (computer science) , sequence (biology) , nuclear magnetic resonance spectroscopy , protein structure , stability (learning theory) , computer science , chemistry , biology , genetics , stereochemistry , machine learning , biochemistry , gene , genotype
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.