Modeling Peptide-Protein Interactions, 1st ed. 2017
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1561

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.

Preface
Table of Contents
Contributing Authors

Part I Prediction of Peptide Binding Sites

Chapter 1
The Usage of ACCLUSTER for Peptide Binding Site Prediction
Chengfei Yan, Xianjin Xu, Xiaoqin Zou

Chapter 2
Detection of Peptide-Binding Sites on Protein Surfaces using the Peptimap Server
Tanggis Bohnuud, Georges Jones, Ora Schueler-Furman, and Dima Kozakov

Chapter 3
Peptide Sub-Optimal Conformation Sampling for the Prediction of Protein-Peptide Interactions
Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, and Pierre Tuffery

Part II Peptide Docking

Chapter 4
Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock
Hasup Lee and Chaok Seok

Chapter 5
Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Protein-Peptide Interactions
Christina Schindler and Martin Zacharias

Chapter 6
Highly Flexible Protein-Peptide Docking Using CABS-Dock
Maciej Paweł Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, and Sebastian Kmiecik

Chapter 7
AnchorDock for Blind Flexible Docking of Peptides to Proteins
Michal Slutzki, Avraham Ben-Shimon, and Masha Y. Niv

Chapter 8
Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK
Cunliang Geng, Siddarth Narasimhan, João P.G.L.M. Rodrigues, and Alexandre M.J.J. Bonvin

Chapter 9
Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock & FlexPepBind
Nawsad Alam and Ora Schueler-Furman

Part III Prediction and Design of Peptide Binding Specificity

Chapter 10
Flexible Backbone Methods for Predicting and Designing Peptide Specificity
Noah Ollikainen

Chapter 11
Simplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models
Fan Zheng and Gevorg Grigoryan

Chapter 12
Binding Specificity Profiles from Computational Peptide Screening
Stefan Wallin

Chapter 13
Enriching Peptide Libraries for Binding Affinity and Specificity through Computationally Directed Library Design
Glenna Wink Foight, T. Scott Chen, Daniel Richman, and Amy E. Keating

Part IV Design of Inhibitory Peptides

Chapter 14
Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite
Jas Bhachoo and Thijs Beuming

Chapter 15
Identifying Loop-Mediated Protein-Protein Interactions using LoopFinder
Timothy R. Siegert, Michael Bird, and Joshua A. Kritzer

Chapter 16
Protein-Peptide Interaction Design: PepCrawler and PinaColada
Daniel Zaidman and Haim J. Wolfson

Chapter 17
Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions
Andrew M. Watkins, Richard Bonneau, and Paramjit S. Arora           

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains keynotes and implementation advice from the experts

Includes supplementary material: sn.pub/extras