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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 Biologyseries 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.
List of contents
Predicting Protein-Protein Interactions using SPRINT.- Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text Mining Protocol.- Construction of Functional Protein Networks using Domain Profile Associations.- Reconstruction of Protein-Protein Interaction Networks using Homology-Based Search: Application to the Autophagy Pathway of Ageing in Podospora anserina.- Predicting Interacting Protein Pairs by Co-Evolutionary Paralog Matching.- A Web-Based Protocol for Inter-Protein Contact Prediction by Deep Learning.- Visual Analysis of Protein-Protein Interaction Docking Models using COZOID Tool.- Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes.- Embedding Alternative Conformations of Proteins in Protein-Protein Interaction Networks.- Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID).- Generation and Interpretationof Context-Specific Human Protein-Protein Interaction Networks with HIPPIE.- Explore Protein-Protein Interactions for Cancer Target Discovery using the OncoPPi Portal.- Perform Pathway Enrichment Analysis using ReactomeFIViz.- De Novo Pathway Enrichment with KeyPathwayMiner.- De Novo Pathway-Based Classification of Breast Cancer Subtypes.- Vienna Graph Clustering.- On TD-WGcluster - Theoretical Foundations and Guidelines for the User.- An Introductory Guide to Aligning Networks using SANA, the Simulated Annealing Network Aligner.
