Protein-Protein Interaction Networks: Methods and Protocols

✍ Scribed by Stefan Canzar, Francisca Rojas Ringeling

• Publisher: Springer US;Humana
• Year: 2020
• Tongue: English
• Leaves: 291
• Series: Methods in Molecular Biology 2074
• Edition: 1st ed. 2020
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
Predicting Protein–Protein Interactions Using SPRINT (Yiwei Li, Lucian Ilie)....Pages 1-11
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 et al.)....Pages 13-34
Construction of Functional Protein Networks Using Domain Profile Associations (Jung Eun Shim, Insuk Lee)....Pages 35-44
Reconstruction of Protein–Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina (Ina Koch, Oliver Philipp, Andrea Hamann, Heinz Osiewacz)....Pages 45-55
Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching (Thomas Gueudré, Carlo Baldassi, Andrea Pagnani, Martin Weigt)....Pages 57-65
A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning (Xiaoyang Jing, Hong Zeng, Sheng Wang, Jinbo Xu)....Pages 67-80
Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool (Jan Byska, Adam Jurcik, Katarina Furmanova, Barbora Kozlikova, Jan J. Palecek)....Pages 81-94
Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes (Genki Terashi, Charles Christoffer, Daisuke Kihara)....Pages 95-112
Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks (Farideh Halakou, Attila Gursoy, Ozlem Keskin)....Pages 113-124
Informed Use of Protein–Protein Interaction Data: A Focus on the Integrated Interactions Database (IID) (Chiara Pastrello, Max Kotlyar, Igor Jurisica)....Pages 125-134
Generation and Interpretation of Context-Specific Human Protein–Protein Interaction Networks with HIPPIE (Gregorio Alanis-Lobato, Martin H. Schaefer)....Pages 135-144
Explore Protein–Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal (Andrey A. Ivanov)....Pages 145-164
Perform Pathway Enrichment Analysis Using ReactomeFIViz (Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu)....Pages 165-179
De Novo Pathway Enrichment with KeyPathwayMiner (Nicolas Alcaraz, Anne Hartebrodt, Markus List)....Pages 181-199
De Novo Pathway-Based Classification of Breast Cancer Subtypes (Markus List, Nicolas Alcaraz, Richa Batra)....Pages 201-213
Vienna Graph Clustering (Sonja Biedermann, Monika Henzinger, Christian Schulz, Bernhard Schuster)....Pages 215-231
On TD-WGcluster: Theoretical Foundations and Guidelines for the User (Angela Re, Paola Lecca)....Pages 233-262
An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner (Wayne B. Hayes)....Pages 263-284
Back Matter ....Pages 285-286

✦ Subjects

Life Sciences; Protein Science; Protein-Ligand Interactions