Protein-Protein Interaction Networks

Methods and Protocols

  • Stefan Canzar
  • Francisca Rojas Ringeling

Part of the Methods in Molecular Biology book series (MIMB, volume 2074)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Kalpana Raja, Jeyakumar Natarajan, Finn Kuusisto, John Steill, Ian Ross, James Thomson et al.
    Pages 13-34
  3. Thomas Gueudré, Carlo Baldassi, Andrea Pagnani, Martin Weigt
    Pages 57-65
  4. Xiaoyang Jing, Hong Zeng, Sheng Wang, Jinbo Xu
    Pages 67-80
  5. Jan Byska, Adam Jurcik, Katarina Furmanova, Barbora Kozlikova, Jan J. Palecek
    Pages 81-94
  6. Genki Terashi, Charles Christoffer, Daisuke Kihara
    Pages 95-112
  7. Farideh Halakou, Attila Gursoy, Ozlem Keskin
    Pages 113-124
  8. Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu
    Pages 165-179
  9. Nicolas Alcaraz, Anne Hartebrodt, Markus List
    Pages 181-199
  10. Markus List, Nicolas Alcaraz, Richa Batra
    Pages 201-213
  11. Sonja Biedermann, Monika Henzinger, Christian Schulz, Bernhard Schuster
    Pages 215-231
  12. Back Matter
    Pages 285-286

About this book


This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.


Y2H data clustering dynamic networks protein complexes topology-based approaches

Editors and affiliations

  • Stefan Canzar
    • 1
  • Francisca Rojas Ringeling
    • 2
  1. 1.Gene CenterLudwig-Maximilians-Universität MünchenMünchenGermany
  2. 2.Gene CenterLudwig-Maximilians-Universität MünchenMünchenGermany

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2020
  • Publisher Name Humana, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-9872-2
  • Online ISBN 978-1-4939-9873-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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