Protein-Protein Interaction Networks: Methods and Protocols

Preface...Table of Contents...Contributing Authors...
1.Predicting Protein-Protein Interactions using SPRINTYiwei Li and Lucian Ilie
2.Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text Mining ProtocolKalpana Raja, Jeyakumar Natarajan, Finn Kuusisto, John Steill, Ian Ross, James Thomson, and Ron Stewart
3.Construction of Functional Protein Networks using Domain Profile AssociationsJung 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 anserinaIna Koch, Oliver Philipp, Andrea Hamann, and Heinz Osiewacz
5.Predicting Interacting Protein Pairs by Co-Evolutionary Paralog MatchingThomas Gueudré, Carlo Baldassi, Andrea Pagnani, and Martin Weigt
6.A Web-Based Protocol for Inter-Protein Contact Prediction by Deep LearningXiaoyang Jing, Hong Zeng, Sheng Wang, and Jinbo Xu
7.Visual Analysis of Protein-Protein Interaction Docking Models using COZOID ToolJ. Byska, A. Jurcik, K. Furmanova, B. Kozlikova, and J.J. Palecek
8.Path-LZerD: Predicting Assembly Order of Multimeric Protein ComplexesGenki Terashi, Charles Christoffer, and Daisuke Kihara
9.Embedding Alternative Conformations of Proteins in Protein-Protein Interaction NetworksFarideh 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 HIPPIEGregorio Alanis-Lobato and Martin H. Schaefer
12.Explore Protein-Protein Interactions for Cancer Target Discovery using the OncoPPi PortalAndrey A. Ivanov
13.Perform Pathway Enrichment Analysis using ReactomeFIVizRobin Haw, Fred Loney, Edison Ong, Yongqun He, and Guanming Wu
14.De Novo Pathway Enrichment with KeyPathwayMinerNicolas Alcaraz, Anne Hartebrodt, and Markus List
15.De Novo Pathway-Based Classification of Breast Cancer SubtypesMarkus List, Nicolas Alcaraz, and Richa Batra
16.Vienna Graph ClusteringSonja 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