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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Acknowledgments
This work has been supported by the French IA bioinformatics BipBip grant (ANR-10-BINF-0003), French Institute for Bioinformatics (IFB) (ANR-11-INBS-0013), and INSERM UMR-S 973 recurrent funding.
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Lamiable, A., Thévenet, P., Eustache, S., Saladin, A., Moroy, G., Tuffery, P. (2017). Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions. In: Schueler-Furman, O., London, N. (eds) Modeling Peptide-Protein Interactions. Methods in Molecular Biology, vol 1561. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6798-8_3
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DOI: https://doi.org/10.1007/978-1-4939-6798-8_3
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