Modeling Peptide-Protein Interactions

Methods and Protocols

  • Ora Schueler-Furman
  • Nir London

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

Table of contents

  1. Front Matter
    Pages i-xi
  2. Prediction of Peptide Binding Sites

    1. Front Matter
      Pages 1-1
    2. Chengfei Yan, Xianjin Xu, Xiaoqin Zou
      Pages 3-9
    3. Tanggis Bohnuud, George Jones, Ora Schueler-Furman, Dima Kozakov
      Pages 11-20
    4. Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, Pierre Tuffery
      Pages 21-34
  3. Peptide Docking

    1. Front Matter
      Pages 35-35
    2. Maciej Paweł Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, Sebastian Kmiecik
      Pages 69-94
    3. Michal Slutzki, Avraham Ben-Shimon, Masha Y. Niv
      Pages 95-108
    4. Cunliang Geng, Siddarth Narasimhan, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
      Pages 109-138
  4. Prediction and Design of Peptide Binding Specificity

  5. Design of Inhibitory Peptides

    1. Front Matter
      Pages 233-233
    2. Timothy R. Siegert, Michael Bird, Joshua A. Kritzer
      Pages 255-277
    3. Daniel Zaidman, Haim J. Wolfson
      Pages 279-290
    4. Andrew M. Watkins, Richard Bonneau, Paramjit S. Arora
      Pages 291-307
  6. Back Matter
    Pages 309-311

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.


peptide binding site prediction peptide-protein docking inhibitory peptides ACCLUSTER PeptiMap AnchorDock and ATTRACT HADDOCK and FlexPepDock loop-mediated protein-protein interactions using LoopFinder PinaColada

Editors and affiliations

  • Ora Schueler-Furman
    • 1
  • Nir London
    • 2
  1. 1.Microbiology and Molecular GeneticsHebrew University Hadassah Medical SchoolJerusalemIsrael
  2. 2.Organic ChemistryThe Weizmann Institute of ScienceRehovotIsrael

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media LLC 2017
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-6796-4
  • Online ISBN 978-1-4939-6798-8
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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