TY - BOOK AU - Wu,Cathy H. AU - Arighi,Cecilia N. AU - Ross,Karen E. TI - Protein bioinformatics: from protein modifications and networks to proteomics T2 - Methods in molecular biology, SN - 9781493967810 U1 - 572/.6 23 PY - 2016///c CY - washington PB - springer science KW - Proteomics KW - Laboratory manuals KW - Bioinformatics KW - Proteins KW - Protein Interaction Maps KW - Protein Folding KW - Computational Biology KW - methods KW - fast KW - Analyse de séquence de protéine KW - méthodes KW - fmesh KW - Biologie informatique KW - Protéines KW - analyse KW - Bases de données de protéines KW - Cartographie d'interactions entre protéines KW - Maturation post-traductionnelle des protéines KW - Protéomique KW - Analyse KW - ram KW - Modifications posttraductionnelles N1 - Includes bibliographical references and index; 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 UR - http://www.springerprotocols.com/BookToc/doi/10.1007/978-1-4939-6783-4 ER -