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Protein Bioinformatics

From Protein Modifications and Networks to Proteomics

  • Book
  • © 2017

Overview

Editors:
  1. Cathy H. Wu

    1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Cecilia N. Arighi

    1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Karen E. Ross

    1. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

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

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Fundamentals of Protein Bioinformatics

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Protein Bioinformatics Databases and Resources

      • Chuming Chen, Hongzhan Huang, Cathy H. Wu
      Pages 3-39

    3. UniProt Protein Knowledgebase

      • Sangya Pundir, Maria J. Martin, Claire O’Donovan
      Pages 41-55

    4. Tutorial on Protein Ontology Resources

      • Cecilia N. Arighi, Harold Drabkin, Karen R. Christie, Karen E. Ross, Darren A. Natale
      Pages 57-78

    5. 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, Christine A. Orengo
      Pages 79-110

    6. Structure-Based Virtual Screening

      • Qingliang Li, Salim Shah
      Pages 111-124

  3. Protein PTM (Post-Translational Modification) Bioinformatics

    1. Front Matter

      Pages 125-125
      Download chapter PDF

    2. Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB

      • Qiuming Yao, Dong Xu
      Pages 127-138

    3. Navigating the Glycome Space and Connecting the Glycoproteome

      • Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek, Nicolle H. Packer
      Pages 139-158

    4. Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins

      • Naila Gulzar, Hayley Dingerdissen, Cheng Yan, Raja Mazumder
      Pages 159-190

    5. Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology

      • Revati Wani, Brion W. Murray
      Pages 191-212

    6. 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 et al.
      Pages 213-232

  4. Protein Network Bioinformatics

    1. Front Matter

      Pages 233-233
      Download chapter PDF

    2. Functional Interaction Network Construction and Analysis for Disease Discovery

      • Guanming Wu, Robin Haw
      Pages 235-253

    3. 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, Attila Gursoy
      Pages 255-270

    4. NDEx: A Community Resource for Sharing and Publishing of Biological Networks

      • Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, Dexter Pratt
      Pages 271-301

    5. Bioinformatics Analysis of Functional Associations of PTMs

      • Pablo Minguez, Peer Bork
      Pages 303-320

    6. Bioinformatics Analysis of PTM-Modified Protein Interaction Networks and Complexes

      • Jonathan Woodsmith, Ulrich Stelzl, Arunachalam Vinayagam
      Pages 321-332

    7. iPTMnet: Integrative Bioinformatics for Studying PTM Networks

      • Karen E. Ross, Hongzhan Huang, Jia Ren, Cecilia N. Arighi, Gang Li, Catalina O. Tudor et al.
      Pages 333-353
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Keywords

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.

Editors and Affiliations

  • Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA

    Cathy H. Wu, Cecilia N. Arighi

  • Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, USA

    Karen E. Ross

Bibliographic Information

  • Book Title: Protein Bioinformatics

  • Book Subtitle: From Protein Modifications and Networks to Proteomics

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

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6783-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-6781-0Published: 03 February 2017

  • Softcover ISBN: 978-1-4939-8299-8Published: 19 July 2018

  • eBook ISBN: 978-1-4939-6783-4Published: 20 January 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 472

  • Number of Illustrations: 3 b/w illustrations, 127 illustrations in colour

  • Topics: Bioinformatics

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