11 good questions and answers about "Secondary structure prediction"

What is the difference between secondary structure assignment and prediction?
  • Assignment: based on 3d structure, eg pdb coordinates, assign structure elements
  • Prediction: based on sequence, predict secondary structure elements
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What distinguishes loops from alfa helices and beta sheets?
  • Very disordered
  • High flexibility
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What are the main differences between α-helices and β-sheets?
  • Alfa helices:
    • local backbone interactions
    • long sequence regions
  • Beta sheets:
    • backbone interactions can be local or distant
    • short sequence regions
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Amino acids have preferences for secondary structure types. Give some examples/key rules.
  • Bulky residues with a Cβ branch tend to favor β-sheets.
  • Smaller amino acids tend to favor α-helices and loops
  • G and P tend to occur at the ends of a helix and in loops
    • (glycine and proline)
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How do you calculate a propensity?
  • Calculate the fraction of a specific residue in a secondary structure type
  • Calculate the fraction of all residues in a secondary structure type
  • Divide the two to get the propensity
    • Propensity < 1: secondary structure type not favored by residue
    • Propensity > 1: secondary structure type favored by residue
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What is the difference between classification and regression?
See slide.

Secondary structure  can be viewed as a classification problem
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Explain the general concept of viewing secondary structure assignment as a classification problem.
See lslide
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What is the concept of double loop cross validation?
See slide
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Explain the difference between parameters and hyperparameters.
  • Parameters: parameters of the model (e.g. variable weights)
  • Hyperparameters: parameters not directly in the model (e.g. number of cross validation loops, size of training and test set)
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Explain "neighbourhood matters!" in the context of secondary strucrure assignment.
  • Residues are not independent of one another
  • Hydrophobicity patterns depending on location of secondary structure element
  • If the residues at positions 5 and 7 of a sequence are both in an alpha-helix, the residue at position 6 is also likely to be an alpha-helix
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Chou-Fasman is an example of a window based approach. Explain.
  • Score every amino acid based on α-helix and β-sheet propensity
  • Look for series of ≥4 amino acids which for example have high scores for α-helix
  • If average α-score > β-score →accept as α-helix


Slinding windows are also used eg GOR method
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