Diploma in Molecular Modelling and Computer aided Drug Design

Subject description :
This paper deals with molecular modeling, quantum mechanics, molecular mechanics
pertaining to drug discovery.
Goals:
Provide a broad and thorough background in modeling tools and docking program
Objectives:
Understand the theories used to build tools and their relationship and basic concepts
involved in drug design.
Unit I
Introduction to the concept of molecular modeling, molecular structure and internal energy,
applications of molecular graphics, coordinate systems, potential energy surfaces,
discussion of local and global energy minima
Unit II
Introduction to computational quantum mechanics: one electron atom, poly electronic
atoms and molecules, Hartree Fock equations; calculating molecular properties using ab
initio and semi empirical methods
Unit III
Molecular mechanics: general features of molecular mechanics force field, bond stretching,
angle bending, torsional terms, non-bonded interactions; force field parametrisation and
transferability; energy minimization: derivative and non-derivative methods, applications
of energy minimization.
Unit IV
Molecular dynamics simulation methods: molecular dynamics using simple models,
molecular dynamics with continuous potential, setting up and running a molecular dynamic
simulation, constraint dynamics; Monte carlo simulation method: Monte Carlo simulation
of molecules.
Unit V
Macromolecular modeling, design of ligands for known macro molecular target sites,
Drug-receptor interaction, classical SAR/QSAR studies and their implications to the 3-D
modeler, 2-D and 3-D database searching, pharmacophore identification and novel drug
design, molecular docking,
Structure-based drug design for all classes of targets.