Protein-Protein Interaction Networks: Methods and Protocols

ISBN-13: 9781493998722 / Angielski / Twarda / 2019 / 286 str.

Stefan Canzar; Francisca Rojas Ringeling

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. Predicting Protein-Protein Interactions using SPRINT

Yiwei Li and Lucian Ilie

2. Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text Mining Protocol

Kalpana Raja, Jeyakumar Natarajan, Finn Kuusisto, John Steill, Ian Ross, James Thomson, and Ron Stewart

3. Construction of Functional Protein Networks using Domain Profile Associations

Jung Eun Shim and Insuk Lee

4. Reconstruction of Protein-Protein Interaction Networks using Homology-Based Search: Application to the Autophagy Pathway of Ageing in Podospora anserina

Ina Koch, Oliver Philipp, Andrea Hamann, and Heinz Osiewacz

5. Predicting Interacting Protein Pairs by Co-Evolutionary Paralog Matching

Thomas Gueudré, Carlo Baldassi, Andrea Pagnani, and Martin Weigt

6. A Web-Based Protocol for Inter-Protein Contact Prediction by Deep Learning

Xiaoyang Jing, Hong Zeng, Sheng Wang, and Jinbo Xu

7. Visual Analysis of Protein-Protein Interaction Docking Models using COZOID Tool

J. Byska, A. Jurcik, K. Furmanova, B. Kozlikova, and J.J. Palecek

8. Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes

Genki Terashi, Charles Christoffer, and Daisuke Kihara

9. Embedding Alternative Conformations of Proteins in Protein-Protein Interaction Networks

Farideh Halakou, Attila Gursoy, and Ozlem Keskin

10. Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID)

Chiara Pastrello, Max Kotlyar, and Igor Jurisica

11. Generation and Interpretation of Context-Specific Human Protein-Protein Interaction Networks with HIPPIE

Gregorio Alanis-Lobato and Martin H. Schaefer

12. Explore Protein-Protein Interactions for Cancer Target Discovery using the OncoPPi Portal

Andrey A. Ivanov

13. Perform Pathway Enrichment Analysis using ReactomeFIViz

Robin Haw, Fred Loney, Edison Ong, Yongqun He, and Guanming Wu

14. De Novo Pathway Enrichment with KeyPathwayMiner

Nicolas Alcaraz, Anne Hartebrodt, and Markus List

15. De Novo Pathway-Based Classification of Breast Cancer Subtypes

Markus List, Nicolas Alcaraz, and Richa Batra

16. Vienna Graph Clustering

Sonja Biedermann , Monika Henzinger , Christian Schulz, and Bernhard Schuster

17. On TD-WGcluster - Theoretical Foundations and Guidelines for the User 

Angela Re and Paola Lecca 

18. An Introductory Guide to Aligning Networks using SANA, the Simulated Annealing Network Aligner 

Wayne B. Hayes 

Blurb

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.