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Many protein-related bioinformatics databases, query tools, and data analysis software tools have been developed to organize and provide biological annotations for proteins to support sequence, structural, functional, and evolutionary analyses in the context of pathway, network, and systems biology. This course provides a working knowledge of various computer-based tools for protein science research. Topics include protein database searching, protein physicochemical properties, secondary structure prediction, statistical verification, post-translational modification (PTM) and networks analysis, protein-protein interaction (PPI) prediction, and bioinformatics approaches in proteomics. Also covered are graphic visualization of the different types of three-dimensional folds and predicting three-dimensional structures by homology methods, machine learning, and neural network analysis. Computer laboratories complement the material presented in lectures. Prerequisites: AS.410.602 Molecular Biology or equivalent, 410.633 Introduction to Bioinformatics; 410.634 Practical Computer Concepts for Bioinformatics.