Protein Bioinformatics

This detailed volume explores techniques for protein bioinformatics research, including databases, software tools, and computational methods, in the context of protein science or proteomics and opening to other omics areas. Beginning with a section on proteogenomics, the book continues by covering posttranslational modifications, processing large-scale mass spectrometry data, protein structure and interactions, as well as protein feature inference. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice to ensure efficacious results.

Authoritative and practical, Protein Bioinformatics serves as an ideal guide for researchers in disciplines encompassing the biotechnological, pharmaceutical, biological, and medical sciences, as well as the computational and engineering sciences.

Exploring the Alternative Proteome with OpenProt and Mass Spectrometry.- Identification of Novel Bacterial Microproteins Encoded by Small Open Reading Frames Using a Computational Proteogenomics Workflow.- Demystifying PTM Identification Using MODplus: Best Practices and Pitfalls.- Understanding PTM Cross-Talk Through a Visualization Tool, PTMViz.- Integrating HexNAcQuest with Glycoproteomics Data Analysis Software to Distinguish HexNAc Isomers on Peptides.- UniCarb-DB, an MS/MS Experimental Glycomic Fragmentation Database.- Integration of Web-Based Tools to Visualize, Integrate, and Interpret Glycogene Expression and Glycomics Data.- PGFinder, an Open Source Software for Peptidoglycomics: The Structural Analysis of Bacterial Peptidoglycan by LC-MS.- Making MS Omics Data ML Ready: SpeCollate Protocols.- AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.- Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.- Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline & ChannelsDB 2.0.- AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses.- Detection and Analysis of Short Linear Motif-Based Protein-Protein Interactions with SLiMAn2 Web Server.- Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods.- SACCHARIS v2: Streamlining Prediction of Carbohydrate-Active Enzyme Specificities Within Large Datasets.- SignalP: The Evolution of a Web Server.