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Full Description
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.
Contents
Protein Bioinformatics Databases and Resources.- UniProt Protein Knowledgebase.- Tutorial on Protein Ontology Resources.- CATH-Gene3D: Generation of the Resource and its Use in Obtaining Structural and Functional Annotations for Protein Sequences.- Structure-Based Virtual Screening.- Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB.- Navigating the Glycome Space and Connecting the Glycoproteome.- Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins.- Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology.- Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.- Functional Interaction Network Construction and Analysis for Disease Discovery.- Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.- NDEx: A Community Resource for Sharing and Publishing of Biological Networks.- Bioinformatics Analysis of Functional Associations of PTMs.- Bioinformatics Analysis of PTM-Modified Protein Interaction Networks and Complexes.- iPTMnet: Integrative Bioinformatics for Studying PTM Networks.- Protein Identification from Tandem Mass Spectra by Database Searching.- Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite.- Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry Proteomic Data: Data to Knowledge Pipelines.- Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.- Computational and Statistical Methods for High-Throughput Mass Spectrometry Based PTMs Analysis.- Cross-Species PTM Mapping from Phosphoproteomic Data.
