title: Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions.
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.
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Lamiable
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Thévenet
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Eustache
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Saladin
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
authors.forename: Gautier
authors.initials: G
authors.lastname: Moroy
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France. pierre.tuffery@univ-paris-diderot.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Tuffery
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D064878:Web Browser
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: Blind docking; PEP-FOLD; PEP-SiteFinder; Peptide conformational sampling; Peptide-protein interactions; Rigid docking