Molecular Modeling & Drug Design

Introduction to Molecular Modeling; What are models used for? Areas of application – Single molecule calculation, Assemblies of molecules; Reaction of the molecules; Drawbacks of mechanical models as compared to graphical models; Co-ordinate systems two – matrix, potential energy surface; Postulates of quantum mechanics, electronic structure calculations, Ab initio, Semi-empirical and Density functional theory calculations, Molecular size versus accuracy; Approximate molecular orbital theories.

Molecular Modeling by Homology, construction of frame work, selecting variable regions, Back bone and side chain placement and refinement, Optimization and validation of protein models. Threading and Ab-initio modeling, Ramchandran plot.

Linear and nonlinear modeled equations, Biological activities, Physicochemical parameters and Molecular descriptors, Application of QSAR modeling in drug discovery.

Introduction to Force field, Use of various parameters for force field calculation (Bond length, angle angle, torsion angle, Electrostatic interaction, Vander waals interactions, Miscellaneous interaction); Introduction Molecular Dynamics using simple models, Dynamics with continuous potentials, Constant temperature and constant dynamics, Conformation searching, Systematic search, Applications to protein folding.

3D pharmacophores modeling, molecular docking, De novo Ligand design, Free energies and solvation, electrostatic and non-electrostatic contribution to free energies; 3D data base searching and virtual screening, Sources of data, molecular similarity and similarity searching, combinatorial libraries – generation and utility. B.Tech. (Biotechnology) 3rd Year Dr. A.P.J. Abdul Kalam Technical University Uttar Pradesh, Lucknow