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TitleModeling Peptide-Protein Interactions [electronic resource] : Methods and Protocols
Author edited by Ora Schueler-Furman, Nir London
ImprintNew York, NY : Springer New York : Imprint: Humana Press, 2017
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Descript XI, 311 p. 87 illus., 68 illus. in color. online resource


This volume covers an array of techniques available for studying peptide-protein docking and design. The book is divided into four sections: peptide binding site prediction; peptide-protein docking; prediction and design of peptide binding specificity; and the design of inhibitory peptides. The chapters in Modeling Peptide-Protein Interactions: Methods and Protocols cover topics such as the usage of ACCLUSTER and PeptiMap for peptide binding site prediction; AnchorDock and ATTRACT for blind, flexible docking of peptides to proteins; flexible peptide docking using HADDOCK and FlexPepDock; identifying loop-mediated protein-protein interactions using LoopFinder; and protein-peptide interaction design using PinaColada. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary details for successful application of the different approaches and step-by-step, readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Modeling Peptide-Protein Interactions: Methods and Protocols provides a diverse and unified overview of this rapidly advancing field of major interest and applicability


The Usage of ACCLUSTER for Peptide Binding Site Prediction -- Detection of Peptide-Binding Sites on Protein Surfaces using the Peptimap Server -- Peptide Sub-Optimal Conformation Sampling for the Prediction of Protein-Peptide Interactions -- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock -- Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Protein-Peptide Interactions -- Highly Flexible Protein-Peptide Docking Using CABS-Dock -- AnchorDock for Blind Flexible Docking of Peptides to Proteins -- Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK -- Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock & FlexPepBind -- Flexible Backbone Methods for Predicting and Designing Peptide Specificity -- SImplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models -- Binding Specificity Profiles from Computational Peptide Screening -- Enriching Peptide Libraries for Binding Affinity and Specificity through Computationally Directed Library Design -- Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite -- Identifying Loop-Mediated Protein-Protein Interactions using LoopFinder -- Protein-Peptide Interaction Design: PepCrawler and PinaColada -- Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions

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