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10 Questions MMDD

Questions of mmdd

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260 views3 pages

10 Questions MMDD

Questions of mmdd

Uploaded by

pavbhaji486
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Group 9- Docking

1)Which of the following techniques in docking is used to predict the preferred orientation of a
ligand to a protein target?

Options:
A) Molecular dynamics simulation
B) Virtual screening
C) Structure-based docking
D) Pharmacophore modeling
Answer: C) Structure-based docking

2)Why are Kollman charges commonly used in molecular docking simulations involving
proteins?

Options:
A) They provide more accurate results by simplifying protein structures.
B) They help represent the partial charges on atoms, improving interaction modeling.
C) They allow for direct simulation of protein denaturation.
D) They are compatible only with rigid docking methods.
Answer: B) They help represent the partial charges on atoms, improving interaction modeling

3)Which of the following statements accurately describes the .pdbqt format?

Options:
A. The .pdbqt format is only used to represent protein structures, not ligands.
B. The .pdbqt format includes information about atom charges and torsional degrees of
freedom.
C. The .pdbqt format is identical to the .pdb format but with added color-coding for each atom.
D. The .pdbqt format does not allow for the representation of polar hydrogen atoms in the
structure.
Answer:
B. The .pdbqt format includes information about atom charges and torsional degrees of
freedom.

4)Which of the following statements accurately describes the .pdbqt format?

Options:
A)The .pdbqt format is only used to represent protein structures, not ligands.
B)The .pdbqt format includes information about atom charges and torsional degrees of freedom.
C)The .pdbqt format is identical to the .pdb format but with added color-coding for each atom.
D)The .pdbqt format does not allow for the representation of polar hydrogen atoms in the
structure.
Answer:
B)The .pdbqt format includes information about atom charges and torsional degrees of freedom.

5)What does the grid box define in AutoDock?

Options:
A) The allowable distance between atoms in a protein structure
B) The region of the receptor where the ligand can bind
C) The temperature during the docking simulation
D) The 3D structure of the ligand
Answer: B) The region of the receptor where the ligand can bind

6)Which method is commonly used in docking to sample different conformations of a flexible


ligand?

Options:
A) Quantum mechanical calculations
B) Genetic algorithms
C) Data mining algorithms
D) Covalent docking techniques
Answer: B) Genetic algorithms

7)In docking, which one is true?

Options:
A) Protein-flexible, ligand-rigid
B) Both protein and ligands are flexible
C) Protein-rigid, ligand flexible
D)All of these
Answer: c) Protein-rigid, ligand flexible

8)Which of the following is typically used in molecular docking to represent the molecular
interactions between a ligand and its target protein?

Options:
A) Energy minimization
B) Molecular dynamics simulations
C) Scoring function
D) Both A and B
Answer: C) Scoring function

9)What is the primary purpose of molecular docking in drug discovery?


Options:
A) To predict the solubility of compounds
B) To determine the binding affinity of a ligand to a target protein
C) To synthesize new compounds
D) To visualize protein structures
Answer - B) To determine the binding affinity of a ligand to a target protein

10)Which of the following factors can influence the accuracy of docking predictions?

Options:
A) The quality of the protein structure used
B) The choice of docking algorithm
C) The scoring function employed
D) All of the above
Answer - D) All of the above (The quality of the protein structure, choice of docking algorithm,
and scoring function all influence accuracy)

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