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Protein Bioinformatics, 1st ed. 2017 From Protein Modifications and Networks to Proteomics Methods in Molecular Biology Series, Vol. 1558

Langue : Anglais

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

Couverture de l’ouvrage Protein Bioinformatics

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.

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
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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
<
<
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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 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 Schwämmle and Marc Vaudel
22. Cross-Species PTM Mapping from Phosphoproteomic Data
Rima Chaudhuri and Jean Yee Hwa Yang
             

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

Date de parution :

Ouvrage de 472 p.

17.8x25.4 cm

Disponible chez l'éditeur (délai d'approvisionnement : 15 jours).

121,31 €

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Date de parution :

Ouvrage de 472 p.

17.8x25.4 cm

Disponible chez l'éditeur (délai d'approvisionnement : 15 jours).

179,34 €

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