Jaypee Institute of Information Technology (JIIT) 2008 B.E Test 3 : Molecular Imaging And Design - Question Paper
JAYPEK UNIVERSITY OF INlrORMATION TECHNOLOGY
WAKNAGHAT, SOLAN, H P
TEST- III, NOVEMBER 2008 SEMESTER V
COURSE CODE: 07B52BU05 MAXM. TIME: 1.30 HRS.
COURSE NAME: MOLECULAR IMAGING AND DESIGN
COURSE CREDIT: 4_MAXM MARKS: 30
Answer all the questions Each question carries equal marks
1. Design a genera) protocol for comparing 2 protein structures: A and B. Discuss any one method of scoring equivalences between them? (5)
2. One day it will be possible to predict the structure of a protein from its scqucncc". Discuss the above statement by considering the principle of Homology method of structure prediction? Discuss the different approaches for optimized the alignment between target and template proteins (a) if sequence similarity between them is less than 40% and (b) if you take multiple templates. (5)
3. What is the basic principle of Threading methods for protein structure prediction? Discuss the various steps for building the structure of a target sequence using threading method. Give example of two online servers for structure prediction. (5)
4. In a protein molecule, if tw'o atoms are separated by 4 or more number of bonds, winch of the following energy terms in the forcefield would contribute to the interaction energy between these two atoms. (5)
a. Bond Energy
b. Angle Energy
c. Dihedral Angle
d. Van der Waals Energy
e. Electrostatic Energy
Write down their functional form (i.e. equation which describes how those interactions vary with distance between atoms).
5. Describe the searching criteria for obtaining the minimum energy state of the molecule based on (a) Steepest Descent and (b) Conjugate gradient minimizers. Which minimizer is comparatively better and why? (5)
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