Protein Bioinformatics

From Protein Modifications and Networks to Proteomics

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

Part of the Methods in Molecular Biology book series (MIMB, volume 1558)

Table of contents

  1. Front Matter
    Pages i-xiv
  2. Fundamentals of Protein Bioinformatics

    1. Front Matter
      Pages 1-1
    2. Chuming Chen, Hongzhan Huang, Cathy H. Wu
      Pages 3-39
    3. Sangya Pundir, Maria J. Martin, Claire O’Donovan
      Pages 41-55
    4. Cecilia N. Arighi, Harold Drabkin, Karen R. Christie, Karen E. Ross, Darren A. Natale
      Pages 57-78
    5. Natalie L. Dawson, Ian Sillitoe, Jonathan G. Lees, Su Datt Lam, Christine A. Orengo
      Pages 79-110
    6. Qingliang Li, Salim Shah
      Pages 111-124
  3. Protein PTM (Post-Translational Modification) Bioinformatics

    1. Front Matter
      Pages 125-125
    2. Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek, Nicolle H. Packer
      Pages 139-158
    3. Naila Gulzar, Hayley Dingerdissen, Cheng Yan, Raja Mazumder
      Pages 159-190
    4. Qinghua Wang, Karen E. Ross, Hongzhan Huang, Jia Ren, Gang Li, K. Vijay-Shanker et al.
      Pages 213-232
  4. Protein Network Bioinformatics

    1. Front Matter
      Pages 233-233
    2. Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, Dexter Pratt
      Pages 271-301
    3. Pablo Minguez, Peer Bork
      Pages 303-320
    4. Jonathan Woodsmith, Ulrich Stelzl, Arunachalam Vinayagam
      Pages 321-332
    5. Karen E. Ross, Hongzhan Huang, Jia Ren, Cecilia N. Arighi, Gang Li, Catalina O. Tudor et al.
      Pages 333-353
  5. Proteomic Bioinformatics

    1. Front Matter
      Pages 355-355
    2. Caroline J. DeHart, Ryan T. Fellers, Luca Fornelli, Neil L. Kelleher, Paul M. Thomas
      Pages 381-394
    3. Erin L. Crowgey, Andrea Matlock, Vidya Venkatraman, Justyna Fert-Bober, Jennifer E. Van Eyk
      Pages 395-413
    4. Hongdong Li, Yang Zhang, Yuanfang Guan, Rajasree Menon, Gilbert S. Omenn
      Pages 415-436
    5. Rima Chaudhuri, Jean Yee Hwa Yang
      Pages 459-469
  6. Back Matter
    Pages 471-472

About this book


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.


protein post-translational modifications protein sequence protein structure protein-protein interactions protein networks computational methods for mass spectrometry-based proteomics alternative splice isoforms databases

Editors and affiliations

  • Cathy H. Wu
    • 1
  • Cecilia N. Arighi
    • 2
  • Karen E. Ross
    • 3
  1. 1.Center for Bioinformatics and Computational BiologyUniversity of DelawareNewarkUSA
  2. 2.Center for Bioinformatics and Computational BiologyUniversity of DelawareNewarkUSA
  3. 3.Department of Biochemistry and Molecular and Cellular BiologyGeorgetown University Medical CenterWashingtonUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media LLC 2017
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-6781-0
  • Online ISBN 978-1-4939-6783-4
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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