| Chapter title |
Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions
|
|---|---|
| Chapter number | 3 |
| Book title |
Modeling Peptide-Protein Interactions
|
| Published in |
Methods in molecular biology, February 2017
|
| DOI | 10.1007/978-1-4939-6798-8_3 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6796-4, 978-1-4939-6798-8
|
| Authors |
Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, Pierre Tuffery |
| Editors |
Ora Schueler-Furman, Nir London |
| Abstract |
The blind identification of candidate patches of interaction on the protein surface is a difficult task that can hardly be accomplished without a heuristic or the use of simplified representations to speed up the search. The PEP-SiteFinder protocol performs a systematic blind search on the protein surface using a rigid docking procedure applied to a limited set of peptide suboptimal conformations expected to approximate satisfactorily the conformation of the peptide in interaction. All steps rely on a coarse-grained representation of the protein and the peptide. While simple, such a protocol can help to infer useful information, assuming a critical analysis of the results. Moreover, such a protocol can be extended to a semi-flexible protocol where the suboptimal conformations are directly folded in the vicinity of the receptor. |
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