JNTUK B.Tech Molecular Modeling and Drug Design gives you detail information of Molecular Modeling and Drug Design R13 syllabus It will be help full to understand you complete curriculum of the year.
UNIT I: INTRODUCTION TO MOLECULAR MODELLING
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.
LO: To describe a detailed note on applications of molecular modeling.
LA: Assessment by developing modeling methods.
UNIT II: QUANTUM MECHANICS
Postulates of quantum mechanics, electronic structure calculations, ab initio, semi-empirical and density functional theory calculations, molecular size versus accuracy. Approximate molecular orbital theories.
LO: To familiarize the term quantum mechanics and its application in molecular modeling.
LA: Assessment by theoretically calculating the mechanism of given molecule.
UNIT III: EMPIRICAL FORCE FIELD MODELS
Molecular Mechanisms, energy calculations, Bond stretch, angle bending, torsional term. Electrostatic interaction- Van der waals interactions. Miscellaneous interaction.
LO: To study the interaction in molecular modeling.
LA: Assessment by evaluating the molecular mechanics of the given molecule.
UNIT IV: MOLECULAR DYNAMICS
Introduction, Molecular Dynamics using simple models. Dynamics with continuous potentials. Constant temperature and constant dynamics. Conformation searching, Systematic search. Applications to protein folding
LO: To understand the molecular dynamics mechanisms.
LA: Assessment by applying molecular dynamics studies to optimize the given molecule.
UNIT V: COMPARATIVE PROTEIN MODELING
Modelling by Homology-the alignment, construction of frame work, selecting variable regions, side chain placement and refinement, validation of protein models –Ramchandran plot, threading and ab initio modeling.
LO: To explain the concept protein modeling by homology modeling and effect of Ramchandran plot, threading and ab initio modeling.
LA: Assessment the ability to compare the effect of homology modeling, Ramchandran plot, threading and Ab initio modeling on protein structure.
UNIT VI: ANALOG AND STRUCTURE BASED DRUG DESIGN
Introduction to QSAR lead module, linear and nonlinear modeled equations, biological activities, physicochemical parameter and molecular descriptors, molecular modelling in drug discovery. 3D pharmacophores ,molecular docking, De novo Ligand design, Free energies and solvation, electrostatic and non-electrostatic contribution to free energies. Applications: 3D data base searching and virtual screening, Sources of data, molecular similarity and similarity searching, combinatorial libraries – generation and utility,
LO: To familiarize various methods involved in drug desining the biological activities and physiochemical properties of drug designing.
LA: Assessment by ability to optimize the molecule by these methods by drug designing.
TEXTBOOKS
- Leach, Principles and applications of modeling, 2nd edition, 2009.
- Hans Pieter, Heltje & Gerd Folkens, Molecular Modeling, 2nd edition, VCH, 2001.
REFERENCES
- Jonathan Goodman, Chemical Applications of Molecular Modeling, 1st edition, royal society of chemistry, 2004.
- Guy H. Grant & W. Graham Richards, Computational Chemistry, 1st edition, Oxford University Press, 1995.
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