Protein Bioinformatics: From Protein Modifications and Networks to Proteomics (Paperback, Softcover Repri)

Preface... Table of Contents... Contributing Authors... Part I Fundamentals of Protein Bioinformatics 1. Protein Bioinformatics Databases and Resources Chuming Chen, Hongzhan Huang, and Cathy H. Wu 2. UniProt Protein Knowledgebase Sangya Pundir, Maria J. Martin, and Claire O'Donovan 3. Tutorial on Protein Ontology Resources Cecilia N. Arighi, Harold Drabkin, Karen R. Christie, Karen E. Ross, and Darren Natale 4. CATH-Gene3D: Generation of the Resource and its Use in Obtaining Structural and Functional Annotations for Protein Sequences Natalie L. Dawson, Ian Sillitoe, Jonathan G. Lees, Su Datt Lam, and Christine A. Orengo 5. Structure-Based Virtual Screening Qingliang Li and Salim Shah Part II Protein PTM (Post-Translational Modification) Bioinformatics 6. Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB Qiuming Yao and Dong Xu 7. Navigating the Glycome Space and Connecting the Glycoproteome Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek, and Nicolle H. Packer 8. Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins Naila Gulzar, Hayley Dingerdissen, Cheng Yan, and Raja Mazumder 9. Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology Revati Wani and Brion W. Murray 10. Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature Qinghua Wang, Karen E. Ross, Hongzhan Huang, Jia Ren, Gang Li, K. Vijay-Shanker, Cathy H. Wu, and Cecilia N. Arighi Part III Protein Network Bioinformatics 11. Functional Interaction Network Construction and Analysis for Disease Discovery Guanming Wu and Robin Haw 12. Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information Nurcan Tuncbag, Ozlem Keskin, Ruth Nussinov, and Attila Gursoy 13. NDEx: A Community Resource for Sharing and Publishing of Biological Networks Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, and Dexter Pratt 14. Bioinformatics Analysis of Functional Associations of PTMs Pablo Minguez and Peer Bork 15. Bioinformatics Analysis of PTM-Modified Protein Interaction Networks and Complexes Jonathan Woodsmith, Ulrich Stelzl, and Arunachalam Vinayagam 16. iPTMnet: Integrative Bioinformatics for Studying PTM Networks Karen E. Ross, Hongzhan Huang, Jia Ren, Cecilia N. Arighi, Gang Li, Catalina O. Tudor, Mengxi Lv, Jung-Youn Lee, Sheng-Chih Chen, K. Vijay-Shanker, and Cathy H. Wu Part IV Proteomic Bioinformatics 17. Protein Identification from Tandem Mass Spectra by Database Searching Nathan J. Edwards 18. Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite Caroline J. DeHart, Ryan T. Fellers, Luca Fornelli, Neil L. Kelleher, and Paul M. Thomas 19. Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry Proteomic Data: Data to Knowledge Pipelines Erin L. Crowgey, Andrea Matloc