GITAM University Molecular Modelling and Drug Design Syllabus
B.Tech. (BT) VII Semester
EURBT732:Departmental Elective: Molecular Modeling and Drug design
Course Code : EURBT 732 Category: DE
Credits: 3 Hours : 3 per week
Quantum chemistry for Modeling of small molecules: Variation method and Time
independent Perturbation theory. Ab initio methods for molecules: Hartree-Fock SCF
method. Common basis sets.
Introduction to semi-empirical methods: Huckel molecular orbital theory. Pariser-
Parr-Pople method. CNDO, AM1 and PM3.
Force fields for molecular modeling: Choice of functional form. Parametrization of a
force field. Anharmonicity. Distributed multipole and polarizable forcefields. The
hydrogen bond. Hydrophobic effect and solvation energy. Potentials of mean force.
Conformational analysis: Geometry optimization using steepest descent and conjugate
gradients. Restrained and constrained molecular dynamics. Distance geometry.
Case studies: Prediction of protein-protein interactions. DNA conformation.
Principles of ligand based drug design: SAR, QSAR and 3D-QSAR. Receptor based
drug design: Principles of receptor based de novo ligand design. Rigid body
Case study: Structure based design of non-peptide inhibitors specific for HIV1
1. Andrew Leach. Molecular modeling: principles and applications. 2nd ed. Pearson
2. Atkins and Friedman. Molecular quantum mechanics. Oxford University Press. 4th