HeroMDAnalysis v5.0 Training Course Quiz
HeroMDAnalysis v5.0 Training Course Quiz
Test your knowledge on computer-aided drug design and molecular dynamics with the HeroMDAnalysis v5.0 Training Course Quiz. This quiz comprises a variety of questions to enhance your understanding of key concepts and applications in the field.
Key Features:
- Multiple-choice format
- Insightful questions covering important topics
- Scoring based on your correct answers
Ques 1. Which out of the following is the most expensive (computationally) technique of computer-aided drug design?
Molecular docking
Pharmacophore mapping
Molecular dynamics
2D-QSAR
Ques 2. Which atoms constitute the backbone of the peptide chain?
Sidechain atoms attached to the Calpha carbon
Only the Calpha carbon atom
Amino group-Calpha-Sidechain atoms
Amino group-Calpha-Carboxyl group
Ques 3. Match the following?
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Column I |
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Column II |
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(i) SASA |
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(a) nM |
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(ii) RMSD |
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(b) indicator of protein structure compactness |
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(iii) Serine |
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(c) A tool to analyze and plot the GROMACS-based MD simulation |
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(iv) GROMACS |
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(d) Å2 |
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(v) HeroMDAnalysis |
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(e) an alcohol group containing amino acid |
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(vi) Radius of Gyration |
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(f) molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids |
(i) – (d); (ii) – (a); (iii) – (e); (iv) – (f); (v) – (c); (vi) – (b).
(i) – (a); (ii) – (e); (iii) – (d); (iv) – (f); (v) – (b); (vi) – (c).
(i) – (b); (ii) – (f); (iii) – (a); (iv) – (e); (v) – (c); (vi) – (d).
(i) – (d); (ii) – (a); (iii) – (e); (iv) – (b); (v) – (c); (vi) – (f).
Ques 4. Which of the following statement is false?
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules.
The protein is a permanently a rigid molecule and the interacting ligand can never induce a conformational change at the binding site.
MD is frequently applied to study the motions of macromolecules such as proteins and nucleic acids.
The binding site in the protein is flexible and the interacting ligand can induce a conformational change at the binding site.
Ques 5. What is the importance of LigFitProt RMSD?
It measures the surface area of a ligand that is accessible to a solvent.
It analyzes the portions of ligand that are fluctuating from their mean structure the most.
It indicates the stability of ligand with the respective protein complex during simulation.
It provides information for the compactness of the protein molecule.
Ques 6. What are the different RMSD values that can be calculated using HeroMDAnalysis?
Ligand and Protein RMSD
Calpha and Backbone RMSD
LigFitProt and ProtFitLig RMSD
Sidechain and Protein RMSD
All of the above
Ques 7. Which of the following is not a requirement to use HeroMDAnalysis?
Linux OS, GROMACS, Xmgrace
.xtc, .edr and .tpr files of MD simulation run
Expertise in the area of command-line interface of using GROMACS
Basic level of knowledge about molecular dynamic simulation
Ques 8. What are the advantages of MD simulation over molecular docking studies?
(a) It helps to understand the behavior of a biomolecule over time.
(b) It provides rich insights into the internal motions of biomolecules.
(c) It is computationally less expensive and less time consuming than molecular docking.
(d) It enables to check the stability of the protein-ligand complex through several parameters such as, thermodynamic parameters, RMSD, RMSF, radius of gyration, etc that are not presented in docking results.
All the statements a), b), c), and d) are correct.
Only statement d) is correct.
The statements a), c), and d) are correct.
The statements a), b), and d) are correct.
Ques 9. When analyzed; the Radius of Gyration and Solvent accessible surface area, both values were found to be decreasing over the duration of simulations. On the other hand, the h-bond interactions Intra-protein were found to be increasing (reference the figure below). Which of the statement can hold true about the system?
The protein has exhibited expansion during the simulation.
The protein has exhibited compaction during the simulation. The water molecules have been displaced out of the binding pockets of the protein.
The water molecules have entered inside the various binding pockets of the protein.
The α-helices and / β-sheets of the protein has loosen and drifted apart.
Ques 10. What of the following pair is not true regarding h-bond interactions?
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Column I |
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Column II |
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(i) Distance |
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Less than 3.0 Å and more than 1.8 Å |
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(ii) Strength |
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More than 75 kcal/mol |
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(iii) Atoms |
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Between hydrogen attached to a highly electronegative atom and small highly electronegative atom |
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(iv) Role |
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The secondary level structure of proteins forms alpha helixes and beta-pleated sheets, which are held together by hydrogen bonds. |
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(v) Angle |
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Close to 170 and 180 degrees have highest strength |
(i), (iii) and (v) are not true.
(ii) and (iv) are not true.
(iii) is not true.
(ii) is not true.
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