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Protein bioinformatics : from protein modifications and networks to proteomics

Author: Cathy H Wu; Cecilia N Arighi; Karen E Ross
Publisher: New York, N.Y. : Humana Press ; Springer, [2017] ©2017
Series: Springer protocols (Series); Methods in molecular biology (Clifton, N.J.), v. 1558.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
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,  Read more...
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Genre/Form: Electronic books
Laboratory manuals
Additional Physical Format: Print version:
Protein bioinformatics.
New York, NY : Humana Press, 2017
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Cathy H Wu; Cecilia N Arighi; Karen E Ross
ISBN: 9781493967834 1493967835
OCLC Number: 971495364
Description: 1 online resource (xiv, 472 pages) : illustrations (chiefly color).
Contents: Protein bioinformatics databases and resources / Chuming Chen, Hongzhan Huang, and Cathy H. Wu --
UniProt protein knowledgebase / Sangya Pundir, Maria J. Martin, and Claire O'Donovan --
Tutorial on protein ontology resources / Cecilia N. Arighi, Harold Drabkin, Karen R. Christie, Karen E. Ross, and Darren A. Natale --
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 --
Structure-based virtual screening / Qingliang Li and Salim Shah --
Bioinformatics analysis of protein phosphorylation in plant systems biology using P3DB / Qiuming Yao and Dong Xu --
Navigating the glycome space and connecting the glycoproteome / Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek, and Nicolle H. Packer --
Impact of nonsynonymous single-nucleotide variations on post-translational modification sites in human proteins / Naila Gulzar, Hayley Dingerdissen, Cheng Yan, and Raja Mazumder --
Analysis of cysteine redox post-translational modifications in cell biology and drug pharmacology / Revati Wani and Brion W. Murray --
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 --
Functional interaction network construction and analysis for disease discovery / Guanming Wu and Robin Haw --
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, and Attila Gursoy --
NDEx : a community resource for sharing and publishing of biological networks / Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, and Dexter Pratt --
Bioinformatics analysis of functional associations of PTMs / Pablo Minguez and Peer Bork --
Bioinformatics analysis of PTM-modified protein interaction networks and complexes / Jonathan Woodsmith, Ulrich Stelzl, and Arunachalam Vinayagam --
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 --
Protein identification from tandem mass spectra by database searching / Nathan J. Edwards --
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 --
Mapping biological networks from quantitative data-independent acquisition mass spectrometry : data to knowledge pipelines / Erin L. Crowgey, Andrea Matlock, Vidya Venkatraman, Justyna Fert-Bober, and Jennifer E. Van Eyk --
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 --
Computational and statistical methods for high-throughput mass spectrometry-based PTM analysis / Veit Schwämmle and Marc Vaudel --
Cross-species PTM mapping from phosphoproteomic data / Rima Chaudhuri and Jean Yee Hwa Yang.
Series Title: Springer protocols (Series); Methods in molecular biology (Clifton, N.J.), v. 1558.
Responsibility: edited by Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross.

Abstract:

This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks.  Read more...

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