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Bioinformatics Practice Test Questions: Secondary Structure Prediction
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Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure.

Topic include: Protein Secondary Structure Prediction for Globular Proteins, Secondary Structure Prediction for Transmembrane Proteins, & Coiled Coil Prediction.

Bioinformatics Practice Test Questions: Secondary Structure Prediction
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25 Questions

1. Which of the following is untrue regarding Chou–Fasman and GOR methods?
2. The early algorithms based their prediction on hydrophobicity scales.
3. Because residues in the same aligned position are assumed to have the same secondary structure, any inconsistencies or errors in prediction of individual sequences can be corrected using a majority rule.
4. Jpred combines the analysis results from six prediction algorithms, including PHD, PREDATOR, DSC, NNSSP, Jnet, and ZPred.
5. Which of the following is untrue regarding Prediction of Helical Membrane Proteins?
6. Which of the following is untrue regarding PSIPRED?
7. The Chou–Fasman algorithm determines the propensity or intrinsic tendency of each residue to be in the helix, strand, and β-turn conformation using observed frequencies found in protein crystal structures.
8. Which of the following is true regarding Prediction of β-Barrel Membrane Proteins?
9. Predictions solely based on hydrophobicity profiles have lowest error rates.
10. Scanning a sequence by hydrophobicity does not reveal transmembrane β-strands.
11. Which of the following is untrue regarding Prediction with Neural Networks?
12. Which of the following is untrue regarding Homology-Based Methods?
13. Which of the following is untrue regarding Prediction with Neural Networks?
14. The structures of this group of proteins, however, are comparatively a lot difficult to resolve either by x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.
15. Prof is not similar to PHD.
16. Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins.
17. Which of the following is untrue regarding PHD?
18. The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E).
19. Which of the following is untrue regarding Coils?
20. Which of the following is untrue regarding the transmembrane proteins?
21. Which of the following is untrue regarding Ab Initio–Based Methods?
22. The secondary structure prediction methods can be either ab initio based, which make use of single sequence information only, or homology based, which makes use of multiple sequence alignment information.
23. In Multicoil, The scoring matrix is constructed based on a database of known three-stranded coiled coils only.
24. Which of the following is untrue regarding TMHMM?
25. The formation of _____ is determined by ______ interactions, whereas the formation of ____ is strongly influenced by ______ interactions.

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