Protein Bioinformatics

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.