Questions and answers for exam Preparation

MCQs

Total Questions : 63 | Page 3 of 7 pages

Question 21. Which of the following is untrue about Shape Complementarity?

The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap
The complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact
The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)
The hydrophobic effect barely has impact on protein folding

Discuss Question

Answer: Option D. -> The hydrophobic effect barely has impact on protein folding
Answer: (d).The hydrophobic effect barely has impact on protein folding

Question 22. In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and α, β, and γ are the translational vectors of the mobile molecule B relative to the static one A.

fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)
fc = \(\sum_{i=0,j=0,k=0}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)
fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,0,0,0 * fBi+αj+βk+ɣ)
fc = \(\sum_{i=0,j=0,k=0}^N\) (f0,i,j,k * fBi+αj+βk+ɣ)

Discuss Question

Answer: Option A. -> fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)
Answer: (a).fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)

Question 23. Which of the following is untrue about Grid Representation?

To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements
To speed up the matching process discretizing the 3-dimensional space using a grid is done
Discretizing allows very fast computer matching using search methods such as Fourier transform
Fourier transform is hardly used in computer matching

Discuss Question

Answer: Option D. -> Fourier transform is hardly used in computer matching
Answer: (d).Fourier transform is hardly used in computer matching

Question 24. In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 25. Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 26. Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option B. -> False
Answer: (b).False

Question 27. In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to the previous step. The probability of accepting the step is given by _________ where ΔE is the difference in energy; kB is Boltzmann’s constant and T the temperature.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 28. Which of the following is true regarding Protein flexibility?

Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only
The Mean Field principle is rarely used in this
Methods have been described for the introduction of side-chain flexibility to protein-protein docking only

Discuss Question

Answer: Option A. -> Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
Answer: (a).Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

Question 29. In a similar way to structure prediction methods models can be evaluated using RMSD to measure the similarity between two molecular complexes.