Questions and answers for exam Preparation

MCQs

Total Questions : 100 | Page 6 of 10 pages

Question 51. Which of the following is untrue about homology modeling?

Homology modeling predicts protein structures based on sequence homology with known structures
It is also known as comparative modeling
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 doesn’t involve the evolutionary distances anywhere

Discuss Question

Answer: Option D. -> It doesn’t involve the evolutionary distances anywhere
Answer: (d).It doesn’t involve the evolutionary distances anywhere

Question 52. Which of the following is untrue about Backbone Model Building Step?

Once optimal alignment is achieved, residues in the aligned regions of the target protein can assume a similar structure as the template proteins
Coordinates of the corresponding residues of the template proteins can be simply copied onto the target protein
If the two residues differ, everything other than the backbone atoms can be copied
If the two aligned residues are identical, coordinates of the side chain atoms are copied along with the main chain atoms

Discuss Question

Answer: Option C. -> If the two residues differ, everything other than the backbone atoms can be copied
Answer: (c).If the two residues differ, everything other than the backbone atoms can be copied

Question 53. Which of the following is untrue about template Selection Step?

The first step in protein structural modeling is to select appropriate structural templates
This forms the foundation for rest of the modeling process
There is no use of heuristic alignment search programs
The template selection involves searching the Protein Data Bank (PDB) for homologous proteins with determined structures

Discuss Question

Answer: Option C. -> There is no use of heuristic alignment search programs
Answer: (c).There is no use of heuristic alignment search programs

Question 54. Which of the following is untrue about Sequence Alignment Step?

Once the structure with the highest sequence similarity is identified as a template, the full-length sequences of the template and target proteins need to be realigned using refined alignment algorithms to obtain optimal alignment
The realignment is the most critical step in homology modeling
The realignment directly affects the quality of the final model
Errors made in the alignment step can be corrected in the following modeling steps

Discuss Question

Answer: Option D. -> Errors made in the alignment step can be corrected in the following modeling steps
Answer: (d).Errors made in the alignment step can be corrected in the following modeling steps

Question 55. Which of the following is untrue about Loop Modeling Step?

In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment
In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment
The gaps cannot be directly modeled
Loop modeling is required for closing the gaps requires

Discuss Question

Answer: Option B. -> In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment
Answer: (b).In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment

Question 56. The procedure begins by measuring the orientation and distance of the anchor regions in the stems and searching PDB for segments of the same length that also match the above endpoint conformation.

True
False
May be True or False
Can't say

Discuss Question

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

Question 57. In Side Chain Refinement step, A side chain can be built by searching every possible conformation at every torsion angle of the side chain to select the one that has the lowest interaction energy with neighboring atoms.

True
False
May be True or False
Can't say

Discuss Question

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

Question 58. Which of the following is untrue about specialized programs for loop modeling?

PETRA is a web server that models loops using the database approach
FREAD is a web server that models loops using the database approach
CODA is a web server that uses a consensus method based on the prediction results from FREAD and PETRA
For loops of three to eight residues, CODA uses consensus conformation of both methods

Discuss Question

Answer: Option A. -> PETRA is a web server that models loops using the database approach
Answer: (a).PETRA is a web server that models loops using the database approach

Question 59. Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.

True
False
May be True or False
Can't say

Discuss Question

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

Question 60. 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.