Syllabus For The Subject MOLECULAR MODELING AND COMPUTER AIDED DRUG DESIGN

UNIT - 01

INTRODUCTION TO THE CONCEPT OF MOLECULAR MODELING - MOLECULAR

STRUCTURE AND INTERNAL ENERGY

UNIT - 02

APPLICATIONS OF MOLECULAR GRAPHICS - COORDINATE SYSTEMS - POTENTIAL

ENERGY SURFACES - DISCUSSION OF LOCAL AND GLOBAL ENERGY MINIMA

UNIT - 03

INTRODUCTION TO COMPUTATIONAL QUANTUM MECHANICS - ONE ELECTRON ATOM -

POLY ELECTRONIC ATOMS AND MOLECULES

UNIT - 04

HARTREE FOCK EQUATIONS - CALCULATING MOLECULAR PROPERTIES USING AB

INITIAL AND SEMI EMPIRICAL METHODS

UNIT - 05

MOLECULAR MECHANICS - GENERAL FEATURES OF MOLECULAR MECHANICS FORCE

FIELD - BOND STRETCHING - ANGLE BENDING - TORSIONAL TERMS - NON-BONDED

INTERACTIONS- - FORCE FIELD PARAMETERIZATION AND TRANSFERABILITY

UNIT - 06

ENERGY MINIMIZATION - DERIVATIVE AND NON-DERIVATIVE METHODS - APPLICATIONS

OF ENERGY MINIMIZATION

UNIT - 07

MOLECULAR DYNAMICS SIMULATION METHODS - MOLECULAR DYNAMICS USING SIMPLE

MODELS - MOLECULAR DYNAMICS WITH CONTINUOUS POTENTIAL - SETTING UP AND

RUNNING A MOLECULAR DYNAMIC SIMULATION - CONSTRAINT DYNAMICS

UNIT - 08

MONTE CARLO SIMULATION METHOD - MONTE CARLO SIMULATION OF MOLECULES

UNIT - 09

MACROMOLECULAR MODELING - DESIGN OF LIGANDS FOR KNOWN MACRO

MOLECULAR TARGET SITES

UNIT - 10

DRUG-RECEPTOR INTERACTION, CLASSICAL SAR/QSAR STUDIES AND THEIR

IMPLICATIONS TO THE 3-D MODELER

UNIT - 11

2-D AND 3-D DATABASE SEARCHING

UNIT - 12

PHARMACOPHORE IDENTIFICATION AND NOVEL DRUG DESIGN - MOLECULAR DOCKING

- STRUCTURE -BASED DRUG DESIGN FOR ALL CLASSES OF TARGETS