Buch, Englisch, Band 1561, 311 Seiten, Book w. online files / update, Format (B × H): 183 mm x 260 mm, Gewicht: 7538 g
Reihe: Methods in Molecular Biology
Methods and Protocols
Buch, Englisch, Band 1561, 311 Seiten, Book w. online files / update, Format (B × H): 183 mm x 260 mm, Gewicht: 7538 g
Reihe: Methods in Molecular Biology
ISBN: 978-1-4939-6796-4
Verlag: Springer
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.
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Weitere Infos & Material
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 Pawel 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
