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How can bioinformatics tools be employed to examine protein structure and function?

Topic

Protein - Information in Action [PROTEOMICS]

Framing Question

How can bioinformatics tools be employed to examine protein structure and function?

Learning Objectives

  • Explain the BLASTP, BLASTX, tBLASTn, tBLASTx algorithms for protein sequence information
  • Interpret the biological significance of an e-value.
  • Describe Hidden Markov Models and how they can be used to assess motifs.
  • Query a dataset with a specific protein sequence to learn about potential functions (e.g. Pfam, CDD, SwissProt, UniProt, etc.).
  • View and interpret the structure output from Protein Data Bank (e.g. Cn3D, Jmol, etc.).
  • Propose potential functions for a give protein structure.
  • Explain the outputs from protein-folding algorithms to predict structure from sequence.
  • Understand how protein structures are determined (e.g. NMR, crystallography).
  • Compare and contrast the output from 2-D gel experiments.
  • Analyze the output from mass spectrometry analysis (e.g., use the MASCOT package).

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