TABLE OF CONTENTS

CHAPTER NO

1.

TITLE

PAGE NO

ABSTRACT

iii

LIST OF TABLE

vi

LIST OF FIGURE

vii

DRUG BINDING DOMAIN

1.1 INTRODUCTION

1.2 PROTEIN BINDING

1.3 DOMAINS ARE UNIT OF

PROTEIN STRUCTURE

1.3.1 Primary structure of domain

1.3.2 Secondary structure of domain

1.3.3 Tertiary structure of domain

1.3.4

Domain and quanternary

Structure

1.4 DOMAIN HAVE LIMIT ON SIZE

4
5

1.5 DOMAINS AS EVOLUTIONARY

MODULE

1.6 MULTIDOMAIN PROTEIN

1.6.1 Orgin

6
6

1.7 DOMAIN ARE AUTONOMOUS

FOLDING

1.7.1 Protein Folding

1.7.2 Advantage of domain in

Protein folding

1.8 DOMAIN AND PROTEIN

FLEXIBILITY

9
4

2.

LITERATURE REVIEW

3.

MATERIAL AND METHOD

10
13

3.1 PROTEIN DATABANK

13

3.2 AUTODOCK

13

3.2.1 Method

14

3.2.1.1. Coordinate file preparation

14

3.2.1.2. Autogrid Calculation

15

3.2.1.3. Docking using AutoDock

15

3.2.1.4. Analysis using AutoDock

4.

Tools

15

RESULT AND DICUSSION

16

4.1 RESULT

16

4.2 DICUSSION

17

4.2.1 Kanamycin

17

4.2.2 Streptomycin

17

4.2.3 Neomycin

18

4.2.4 Gentamicin

18

4.2.5 Netilmicin

19

REFERENCE

TABLE NO

LIST OF TABLES

PAGE NO
4.1

Result for docking studies

vi

17

FIGURE NO

LIST OF FIGURES

PAGE NO
4.1

Kanamycin bound to ribosomal protein

17

residue Arg82 and Gln28

4.2

Streptomycin bound to ribosomal protein

residue Gly68 and Arg49

4.3

Neomycin bound to ribosomal protein

residue Gly68 and Asp88

4.4

18

Gentamicin bound to ribosomal protein

residue Arg82 and Asp88

4.5

18

19

Nelilmicin bound to ribosomal protein

residue Arg49 and Asp88

vii

19