Protein bioinformatics : from protein modifications and networks to proteomics

著者

• Wu, Cathy H.
• Arighi, Cecilia N.
• Ross, Karen E.

書誌事項

Protein bioinformatics : from protein modifications and networks to proteomics

edited by Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross

（Methods in molecular biology / John M. Walker, series editor, 1558）（Springer protocols）

Humana Press, c2017

注記

Includes bibliographical references and index

内容説明・目次

内容説明

This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks. This book is organized into four parts and covers the basic framework and major resources for analysis of protein sequence, structure, and function; approaches and resources for analysis of protein PTMs, protein-protein interactions (PPIs) and protein networks, including tools for PPI prediction and approaches for the construction of PPI and PTM networks; and bioinformatics approaches in proteomics, including computational methods for mass spectrometry-based proteomics and integrative analysis for alternative splice isoforms, for functional discovery. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory or computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein Bioinformatics: From Protein Modifications and Networks to Proteomics is a valuable resource for readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods, and future trends in protein and proteomic data analysis in systems biology. This book is useful to researchers who work in the biotechnology and pharmaceutical industries, and in various academic departments, such as biological and medical sciences and computer sciences and engineering.

目次

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 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 Matlock, Vidya Venkatraman, Justyna Fert-Bober, and Jennifer E. Van Eyk 20. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks Hongdong Li, Yang Zhang, Yuanfang Guan, Rajasree Menon, and Gilbert S. Omenn 21. Computational and Statistical Methods for High-Throughput Mass Spectrometry Based PTMs Analysis Veit Schwammle and Marc Vaudel 22. Cross-Species PTM Mapping from Phosphoproteomic Data Rima Chaudhuri and Jean Yee Hwa Yang

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詳細情報

• NII書誌ID(NCID): BB23430021
• ISBN:
  • 9781493967810
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York
• ページ数/冊数: xiv, 472 p.
• 大きさ: 27 cm
• 親書誌ID:
  • BA10794673
  • BA88873632