Which of the following is true regarding Protein flexibility?

Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

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

Which_of_the_following_is_true_regarding_Protein_flexibility?$

Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

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

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.

high-energy conformations, prior to

low-energy conformations, after

low-energy conformations, prior to

high-energy conformations, prior to

high-energy conformations, after

In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

large molecule, highly flexible

small molecule, highly flexible

large molecule, highly flexible

Proteins are dynamic entities that undergo _______

illimitable or total conformational change of amino acid side-chains when in solution

only fluctuation of flexible loop regions about equilibrium positions when in solution

only limited conformational change of amino acid side-chains when in solution

both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution

illimitable or total conformational change of amino acid side-chains when in solution

14 + Mcqs in Conformational Flexibility in Bioinformatics Page 1 McqOptions

1.	Which of the following is true regarding Protein flexibility?
A.	Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
B.	Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only
C.	The Mean Field principle is rarely used in this
D.	Methods have been described for the introduction of side-chain flexibility to protein-protein docking only
Answer» B. Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

Discussion

2.	Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.
A.	True
B.	False
Answer» C.

Discussion

3.	Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.
A.	True
B.	False
Answer» B. False

Discussion

4.	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.
A.	True
B.	False
Answer» B. False

Discussion

5.	The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.
A.	N +1
B.	N
C.	N2
D.	N/2
Answer» C. N2

Discussion

6.	STOCHASTIC_METHODS_CAN_GUARANTEE_REACHING_A_GLOBAL_OPTIMAL_SOLUTION_AND_THE_METHODS_ARE_COMPUTATIONALLY_COSTLY_IN_COMPARISON_TO_THE_OTHER_METHODS.?$
A.	True
B.	False
Answer» C.

Discussion

7.	Which_of_the_following_is_true_regarding_Protein_flexibility?$
A.	Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
B.	Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only
C.	The Mean Field principle is rarely used in this
D.	Methods have been described for the introduction of side-chain flexibility to protein-protein docking only
Answer» B. Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

Discussion

8.	Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members?
A.	True
B.	False
Answer» B. False

Discussion

9.	In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.
A.	True
B.	False
Answer» B. False

Discussion

10.	The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ___ ligand conformations. Where, the N is the number of low-energy conformations.
A.	N +1
B.	N
C.	N<sup>2</sup>
D.	N/2
Answer» C. N<sup>2</sup>

Discussion

11.	In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.
A.	low-energy conformations, after
B.	low-energy conformations, prior to
C.	high-energy conformations, prior to
D.	high-energy conformations, after
Answer» C. high-energy conformations, prior to

Discussion

12.	In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.
A.	small molecule, highly flexible
B.	large molecule, highly flexible
C.	large molecule, more flexible
D.	small molecule, less flexible
Answer» B. large molecule, highly flexible

Discussion

13.	Typical motions of proteins will be primarily treated by a rigid body model for docking.
A.	True
B.	False
Answer» C.

Discussion

14.	Proteins are dynamic entities that undergo _______
A.	only fluctuation of flexible loop regions about equilibrium positions when in solution
B.	only limited conformational change of amino acid side-chains when in solution
C.	both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution
D.	illimitable or total conformational change of amino acid side-chains when in solution
Answer» D. illimitable or total conformational change of amino acid side-chains when in solution

Discussion

Explore topic-wise MCQs in Bioinformatics.

Which of the following is true regarding Protein flexibility?

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

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

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.

The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.

STOCHASTIC_METHODS_CAN_GUARANTEE_REACHING_A_GLOBAL_OPTIMAL_SOLUTION_AND_THE_METHODS_ARE_COMPUTATIONALLY_COSTLY_IN_COMPARISON_TO_THE_OTHER_METHODS.?$

Which_of_the_following_is_true_regarding_Protein_flexibility?$

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

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

The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ___ ligand conformations. Where, the N is the number of low-energy conformations.

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different ___ that are computed _ the ligand being docked into the receptor.

In case of Protein-ligand docking, __ ligands are often _ in adapting their shape to fit the receptor binding pocket.

Typical motions of proteins will be primarily treated by a rigid body model for docking.

Proteins are dynamic entities that undergo _______