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Protein Bioinformatics [electronic resource]: From Protein Modifications and Networks to Proteomics

edited by Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross
Format
EBook; Book; Online
Published
New York : Humana Press, [2017]
Language
English
Uniform Title
Protein Bioinformatics (Wu)
Series
Methods in Molecular Biology
Springer Protocols
Methods in Molecular Biology (Clifton, N.J.)
Springer Protocols (Series)
ISBN
9781493967810, 1493967819, 9781493967834 (ebook), 1493967835, 9781493967834
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.
Description
Mode of access: World wide Web.
Notes
Includes bibliographical references and index.
Series Statement
Methods in molecular biology, 1064-3745 ; 1558
Methods in molecular biology (Clifton, N.J.) ; v. 1558. 1064-3745
Copyright Not EvaluatedCopyright Not Evaluated
Technical Details
  • Access in Virgo Classic
  • Staff View

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    t| Protein bioinformatics databases and resources / r| Chuming Chen, Hongzhan Huang, and Cathy H. Wu -- t| UniProt protein knowledgebase / r| Sangya Pundir, Maria J. Martin, and Claire O'Donovan -- t| Tutorial on protein ontology resources / r| Cecilia N. Arighi, Harold Drabkin, Karen R. Christie, Karen E. Ross, and Darren A. Natale -- t| CATH-Gene3D : generation of the resource and its use in obtaining structural and functional annotations for protein sequences / r| Natalie L. Dawson, Ian Sillitoe, Jonathan G. Lees, Su Datt Lam, and Christine A. Orengo -- t| Structure-based virtual screening / r| Qingliang Li and Salim Shah -- t| Bioinformatics analysis of protein phosphorylation in plant systems biology using P3DB / r| Qiuming Yao and Dong Xu -- t| Navigating the glycome space and connecting the glycoproteome / r| Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Julien Mariethoz, Frederique Lisacek, and Nicolle H. Packer -- t| Impact of nonsynonymous single-nucleotide variations on post-translational modification sites in human proteins / r| Naila Gulzar, Hayley Dingerdissen, Cheng Yan, and Raja Mazumder -- t| Analysis of cysteine redox post-translational modifications in cell biology and drug pharmacology / r| Revati Wani and Brion W. Murray -- t| Analysis of protein phosphorylation and its functional impact on protein-protein interactions via text mining of the scientific literature / r| Qinghua Wang, Karen E. Ross, Hongzhan Huang, Jia Ren, Gang Li, K. Vijay-Shanker, Cathy H. Wu, and Cecilia N. Arighi -- t| Functional interaction network construction and analysis for disease discovery / r| Guanming Wu and Robin Haw -- t| Prediction of protein interactions by structural matching : prediction of PPI networks and the effects of mutations on PPIs that combines sequence and structural information / r| Nurcan Tuncbag, Ozlem Keskin, Ruth Nussinov, and Attila Gursoy -- t| NDEx : a community resource for sharing and publishing of biological networks / r| Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, and Dexter Pratt -- t| Bioinformatics analysis of functional associations of PTMs / r| Pablo Minguez and Peer Bork -- t| Bioinformatics analysis of PTM-modified protein interaction networks and complexes / r| Jonathan Woodsmith, Ulrich Stelzl, and Arunachalam Vinayagam -- t| iPTMnet : integrative bioinformatics for studying PTM networks / r| 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 -- t| Protein identification from tandem mass spectra by database searching / r| Nathan J. Edwards -- t| Bioinformatics analysis of top-down mass spectrometry data with ProSight Lite / r| Caroline J. DeHart, Ryan T. Fellers, Luca Fornelli, Neil L. Kelleher, and Paul M. Thomas -- t| Mapping biological networks from quantitative data-independent acquisition mass spectrometry : data to knowledge pipelines / r| Erin L. Crowgey, Andrea Matlock, Vidya Venkatraman, Justyna Fert-Bober, and Jennifer E. Van Eyk -- t| Annotation of alternatively spliced proteins and transcripts with protein-folding algorithms and isoform-level functional networks / r| Hongdong Li, Yang Zhang, Yuanfang Guan, Rajasree Menon, and Gilbert S. Omenn -- t| Computational and statistical methods for high-throughput mass spectrometry-based PTM analysis / r| Veit Schwämmle and Marc Vaudel -- t| Cross-species PTM mapping from phosphoproteomic data / r| Rima Chaudhuri and Jean Yee Hwa Yang.
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