Protein-Protein Interaction Networks

Chapter 1 Predicting Protein–Protein Interactions Using SPRINT

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

Chapter 3 Construction of Functional Protein Networks Using Domain Profile Associations

Chapter 4 Reconstruction of Protein–Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina

Chapter 5 Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching

Chapter 6 A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning

Chapter 7 Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool

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

Chapter 9 Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks

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

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

Chapter 12 Explore Protein–Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal

Chapter 13 Perform Pathway Enrichment Analysis Using ReactomeFIViz

Chapter 14 De Novo Pathway Enrichment with KeyPathwayMiner

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

Chapter 16 Vienna Graph Clustering

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

Chapter 18 An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner