Book Volume 1558 2017

Protein Bioinformatics

From Protein Modifications and Networks to Proteomics

Editors:

ISBN: 978-1-4939-6781-0 (Print) 978-1-4939-6783-4 (Online)

Table of contents (22 protocols)

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  1. Front Matter

    Pages i-xiv

  2. Fundamentals of Protein Bioinformatics

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 3-39

      Protein Bioinformatics Databases and Resources

    3. No Access

      Protocol

      Pages 41-55

      UniProt Protein Knowledgebase

    4. No Access

      Protocol

      Pages 57-78

      Tutorial on Protein Ontology Resources

    5. No Access

      Protocol

      Pages 79-110

      CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences

    6. No Access

      Protocol

      Pages 111-124

      Structure-Based Virtual Screening

  3. Protein PTM (Post-Translational Modification) Bioinformatics

    1. Front Matter

      Pages 125-125

    2. No Access

      Protocol

      Pages 127-138

      Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB

    3. No Access

      Protocol

      Pages 139-158

      Navigating the Glycome Space and Connecting the Glycoproteome

    4. No Access

      Protocol

      Pages 159-190

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

    5. No Access

      Protocol

      Pages 191-212

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

    6. No Access

      Protocol

      Pages 213-232

      Analysis of Protein Phosphorylation and Its Functional Impact on Protein–Protein Interactions via Text Mining of the Scientific Literature

  4. Protein Network Bioinformatics

    1. Front Matter

      Pages 233-233

    2. No Access

      Protocol

      Pages 235-253

      Functional Interaction Network Construction and Analysis for Disease Discovery

    3. No Access

      Protocol

      Pages 255-270

      Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information

    4. No Access

      Protocol

      Pages 271-301

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

    5. No Access

      Protocol

      Pages 303-320

      Bioinformatics Analysis of Functional Associations of PTMs

    6. No Access

      Protocol

      Pages 321-332

      Bioinformatics Analysis of PTM-Modified Protein Interaction Networks and Complexes

    7. No Access

      Protocol

      Pages 333-353

      iPTMnet: Integrative Bioinformatics for Studying PTM Networks

  5. Proteomic Bioinformatics

    1. Front Matter

      Pages 355-355

    2. No Access

      Protocol

      Pages 357-380

      Protein Identification from Tandem Mass Spectra by Database Searching

    3. No Access

      Protocol

      Pages 381-394

      Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite

    4. No Access

      Protocol

      Pages 395-413

      Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines

    5. No Access

      Protocol

      Pages 415-436

      Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks

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