Protein-Protein Interaction Networks: Methods and Protocols

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