Secondary structure prediction
11 important questions on 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
What distinguishes loops from alfa helices and beta sheets?
- Very disordered
- High flexibility
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)
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
What is the difference between classification and regression?
Secondary structure can be viewed as a classification problem
Explain the general concept of viewing secondary structure assignment as a classification problem.
What is the concept of double loop cross validation?
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)
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
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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