Reference : In silico predictions of 3D structures of linear and cyclic peptides with natural and no...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/2268/108392
In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
English
Beaufays, Jérôme [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
Lins, Laurence mailto [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
Thomas, Annick [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
Brasseur, Robert mailto [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
2012
Journal of Peptide Science : An Official Publication of the European Peptide Society
John Wiley & Sons, Inc
18
1
17-24
Yes (verified by ORBi)
International
1075-2617
Chichester
United Kingdom
[en] We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd.
http://hdl.handle.net/2268/108392
10.1002/psc.1410
Laurence Lins est 1er co-auteur

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