How well does sequence similarity predict similarity in binding specificity?

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  • Title: "How well does sequence similarity predict similarity in binding specificity?"
  • Paper to be examined: “A Specificity Map for the PDZ Domain Family”, PLoS Biol 6(9): e239 [1]
  • Key claim of the paper: "Similarity in sequence of binding motifs of PDZ domains can be used to identify 16 distinct specificity classes."
  • Data and Instructions
    • Download all the raw data needed for this module at:
    • Try opening the LOLA software (see instruction in README.txt).
    • Make sure R is installed in your computer
    • Make sure you have Java
  • Schedule:
    • H1: General intro to the paper/motivation
    • H2-3: Write code to import the data and compute the Position Weight Matrices (PWM).
    • H4-6: Write code to compute and compare different types of similarity values and do the clustering.
    • H7: Use the LOLA visualization software to look at the data.
    • H8: Start writing the report
    • H9: Broader view on the use and challenges with similarity metrics in biology, and other applications of the mathematical tools developed in this paper.
  • Key bioinformatics concept of this module:
    • Similarity measures between biological objects (here protein sequence and binding specificity)
    • Clustering