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Modeling Peptide-Protein Interactions

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Ora Schueler-Furman

    1. Microbiology and Molecular Genetics, Hebrew University Hadassah Medical School, Jerusalem, Israel

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    You can also search for this editor in PubMed   Google Scholar

  2. Nir London

    1. Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1561)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Prediction of Peptide Binding Sites

    1. Front Matter

      Pages 1-1
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    2. The Usage of ACCLUSTER for Peptide Binding Site Prediction

      • Chengfei Yan, Xianjin Xu, Xiaoqin Zou
      Pages 3-9

    3. Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

      • Tanggis Bohnuud, George Jones, Ora Schueler-Furman, Dima Kozakov
      Pages 11-20

    4. Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions

      • Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, Pierre Tuffery
      Pages 21-34

  3. Peptide Docking

    1. Front Matter

      Pages 35-35
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    2. Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock

      • Hasup Lee, Chaok Seok
      Pages 37-47

    3. Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions

      • Christina Schindler, Martin Zacharias
      Pages 49-68

    4. Highly Flexible Protein-Peptide Docking Using CABS-Dock

      • Maciej PaweÅ‚ Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, Sebastian Kmiecik
      Pages 69-94

    5. AnchorDock for Blind Flexible Docking of Peptides to Proteins

      • Michal Slutzki, Avraham Ben-Shimon, Masha Y. Niv
      Pages 95-108

    6. Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK

      • Cunliang Geng, Siddarth Narasimhan, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
      Pages 109-138

    7. Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind

      • Nawsad Alam, Ora Schueler-Furman
      Pages 139-169

  4. Prediction and Design of Peptide Binding Specificity

    1. Front Matter

      Pages 171-171
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    2. Flexible Backbone Methods for Predicting and Designing Peptide Specificity

      • Noah Ollikainen
      Pages 173-187

    3. Simplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models

      • Fan Zheng, Gevorg Grigoryan
      Pages 189-200

    4. Binding Specificity Profiles from Computational Peptide Screening

      • Stefan Wallin
      Pages 201-211

    5. Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design

      • Glenna Wink Foight, T. Scott Chen, Daniel Richman, Amy E. Keating
      Pages 213-232

  5. Design of Inhibitory Peptides

    1. Front Matter

      Pages 233-233
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    2. Investigating Protein–Peptide Interactions Using the Schrödinger Computational Suite

      • Jas Bhachoo, Thijs Beuming
      Pages 235-254

    3. Identifying Loop-Mediated Protein–Protein Interactions Using LoopFinder

      • Timothy R. Siegert, Michael Bird, Joshua A. Kritzer
      Pages 255-277
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Keywords

About this book

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.

 

Editors and Affiliations

  • Microbiology and Molecular Genetics, Hebrew University Hadassah Medical School, Jerusalem, Israel

    Ora Schueler-Furman

  • Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel

    Nir London

Bibliographic Information

  • Book Title: Modeling Peptide-Protein Interactions

  • Book Subtitle: Methods and Protocols

  • Editors: Ora Schueler-Furman, Nir London

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6798-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-6796-4Published: 27 February 2017

  • Softcover ISBN: 978-1-4939-8302-5Published: 15 July 2018

  • eBook ISBN: 978-1-4939-6798-8Published: 23 February 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 311

  • Number of Illustrations: 19 b/w illustrations, 68 illustrations in colour

  • Topics: Protein Science

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