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Title Protein bioinformatics : from protein modifications and networks to proteomics / edited by Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross
Published New York, N.Y. : Humana Press : Springer, [2017]


Description 1 online resource (xiv, 472 pages) : illustrations (chiefly color)
Series Springer protocols
Methods in molecular biology, 1940-6029 ; 1558
Springer protocols (Series)
Methods in molecular biology (Clifton, N.J.) ; v. 1558. 1064-3745
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
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, 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
Bibliography Includes bibliographical references and index
Notes Online resource; title from PDF title page (SpringerProtocol, viewed February 6, 2017)
Subject Proteomics -- Laboratory manuals
Bioinformatics -- Laboratory manuals
Proteins -- Laboratory manuals
Protein Interaction Maps
Protein Folding
Computational Biology -- methods
Molecular biology.
Science -- Life Sciences -- Anatomy & Physiology.
Analyse de séquence de protéine -- méthodes.
Biologie informatique -- méthodes.
Protéines -- analyse.
Bases de données de protéines.
Cartographie d'interactions entre protéines -- analyse.
Maturation post-traductionnelle des protéines.
Protéomique -- méthodes.
Protéines -- Analyse.
Protéines -- Modifications posttraductionnelles.
Genre/Form Laboratory manuals
Laboratory manuals.
Form Electronic book
Author Wu, Cathy H., editor
Arighi, Cecilia N., editor
Ross, Karen E., editor
ISBN 9781493967834