M.Sc. DEGREE EXAMINATION, APRIL 2016
Second Semester
Bioinformatics
MOLECULAR MODELING AND
PHARMACOINFORMATICS
(2013 onwards)
Time 3 Hours Maximum 75 Marks
Part A (10 2 20)
Answer all questions.
1. What is a lead molecule?
2. List different types of drug targets.
3. What is potential energy surface?
4. List any four force fields used in molecular modeling.
5. What is periodic boundary condition?
6. What is a template structure?
7. When structure-based drug design cannot be applied?
8. List any four descriptors used in QSAR.
9. What is a prodrug?
10. When Lipinski's rule fails?
Sub. Code
502203
RW-10866
2
Ws5
Part B 5 25)
Answer all questions choosing either or
11. Explain the role of bioinformatics for the
identification of new drug targets.
Or
How will you optimize a lead molecule?
12. Difference between Morse and Harmonic potential.
Or
Describe steepest descent and conjugate gradient
methods.
13. Explain Implicit and Explicit solvation models.
Or
Write about protein folding.
14. What are the steps involved in de novo drug design?
Or
How will you construct a pharmacophore model and
use for lead identification?
15. How drugs act? Explain.
Or
Write about ADME properties of a drug.
RW-10866
3
Ws5
Part C 10 30)
Answer any three questions.
16. What are the steps involved in discovering a new drug?
Explain the role of in silico methods for drug design.
17. Explain in detail bonded and non-bonded interactions.
18. How will you construct a 3D protein model and validate
it? Explain in a stepwise manner.
19. Write in detail various search and scoring algorithms
used in docking. How docking is used for designing a
drug?
20. How are drugs removed from our body? Explain in detail
with a diagram.