Bioinformatics Practice Test 4

1. Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins.

False

True

2. Which of the following is true regarding Prediction of β-Barrel Membrane Proteins?

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophilic in nature

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophobic in nature

They contain six to nine residues

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are amphipathic in nature

3. The energy necessary to form individual base pairs is not quite affected by adjacent base pairs.

True

False

4. 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.

True

False

5. The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.

True

False

6. Which of the following is an incorrect statement?

Molscript is a UNIX program capable of generating wire-frame

In particular, secondary structure elements can be drawn with solid spirals and arrows representing α-helices and β-strands, respectively

Molscript is capable of generating space-filling

Molscript is not capable of generating ball-and-stick styles

7. The root mean square deviation (RMSD), without the size dependency correction is?

\(\sum_{i=1}^N \frac{D_i^2}{N + 1}\)

\(\sum_{i=1}^N \frac{D_i^2}{N x N}\)

\(\sum_{i=1}^N \frac{D_i^2}{N - 1}\)

\(\sum_{i=1}^N \frac{D_i^2}{N}\)

8. In the step of Model Refinement Using Energy Function, the structural irregularities can be corrected by applying the energy minimization procedure on the entire model, which moves the atoms in such a way that the overall conformation has the lowest energy potential.

False

True

9. Which of the following is untrue regarding Prediction with Neural Networks?

It is used to analyze substitution patterns in multiple sequence alignments

It is not a machine learning process

The third-generation prediction algorithms extensively apply sophisticated neural networks

It requires a structure of multiple layers of interconnected variables or nodes

10. Which of the following is untrue about homology modeling?

Homology modeling predicts protein structures based on sequence homology with known structures

The principle behind it is that if two proteins share a high enough sequence similarity, they are likely to have very similar three-dimensional structures

It is also known as comparative modeling

It doesn’t involve the evolutionary distances anywhere