| Description |
1 online resource (xi, 286 pages) : illustrations (some color) |
| Series |
Methods in molecular biology, 1940-6029 ; volume 2074 |
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Methods in molecular biology (Clifton, N.J.) ; v. 2074. 1064-3745
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| Contents |
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 |
| Summary |
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 |
| Bibliography |
Includes bibliographical references and index |
| Notes |
Online resource; title from PDF title page (SpringerLink, viewed October 8, 2019) |
| Subject |
Protein-protein interactions -- Laboratory manuals
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Protein-protein interactions
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| Genre/Form |
Laboratory manuals
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Laboratory manuals.
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Manuels de laboratoire.
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| Form |
Electronic book
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| Author |
Canzar, Stefan, editor
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Ringeling, Francisca Rojas, editor
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| ISBN |
9781493998739 |
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1493998730 |
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