Modeling Peptide-Protein Interactions Methods and Protocols [Paperback]

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-PeplCÝ