Molecular Mechanics:
Introduction, The Morse Potential, The Harmonic Oscillator Model for Molecules, Comparison of Morse and Harmonic Potential, Two atoms connected by a bond, Poly atomic Molecules, Energy due to Stretch, Bend, Stretch-Bend, Torsional strain, van der Waals and Dipole-Diploe interactions. Types of Potentials: Lennard-Jones, Truncated Lennard-jones, Exponential-6, Ionic and Polar potentials. Types of Force Fields: AMBER, CHARMM, Merck Molecular Force Field, Consistent Force Field, MM2, MM3 and MM4 force fields.
Potential Energy Surface:
Convergence Criteria, Characterizing Stationary Points, Search for Transition States. Optimization:- multivariable Optimization Algorithms, level Sets, Level Curves, Gradients, Optimization Criteria, Unidirectional Search, Finding Minimum Point, Gradient based Methods-Steepest Descent and Conjugate Gradient Methods
Molecular Dynamics Simulation:
Introduction, Radial distribution functions, Pair Correlation function, Newtonian dynamics, Integrators- Leapfrog and Verlet algorithm, Potential truncation and shifted-force potentials, Implicit and explicit Solvation models, Periodic boundary conditions, Temperature and pressure control in molecular dynamics simulations
Molecular modeling in Drug design:
Conformational analysis, lead identification, optimization and validation. Methods and Tools in Computer-aided molecular Design, Analog Based drug design:-Pharmacophores and QSAR. Structure based drug design:- Docking, De Novo Drug Design, Virtual screening.
Structure Activity Relationship:
Introduction to QSAR, QSPR, Various Descriptors used in QSARs, Regression Analysis, Significance and Validity of QSAR Regression Equations, Partial Least Squares (PLS) Analysis, Multi Linear Regression Analysis. Application of Genetic Algorithms, Neural Networks and Principle Components Analysis in QSAR analysis.
Course outcomes:
At the end of the course the student will be able to:
Question paper pattern:
The SEE question paper will be set for 100 marks and the marks scored will be proportionately reduced to 60.
Textbook/ Textbooks
1 Computational Chemistry and Molecular Modelling-Principles and Applications Ramachandran, Deepa and Namboodri, Springer_Verlag. 2008
2 Mathematical Approaches to Biomolecular Structure and Dynamics Jill P. Mesirov, Klaus Schulten, De Witt L. Sumners Springer 1996.
Reference Books
1 Molecular Modeling for Beginners. Alan Hinchliffe John Wiley & Sons Ltd. (2nd Edition), 2008
2 Foundations of Molecular Modeling and Simulation. Peter T. Cummings, Phillip R.Westmorland, Brice Carnahan, American Institute of Chemical Engineers 2001
3 New Algorithms for Macromolecular Simulation Timothy J. Barth, Michael Griebel, David E.Keyes, Risto M. Nieminen, Dirk Roose, Tamar Schlick, Springer 2011