B. Tech Biosciences and Bioengineering

BT 305        Computational Biology        2-0-2-6

 

 

Syllabus: Analysis of protein content and organization; Analysis of protein structures, comparative modeling, structure prediction algorithms and tools, threading empirical force field models; Bond stretching, angle bending and torsional terms, the harmonic oscillator model for molecules. Non-bonded interactions; Van der Waals, electrostatic and hydrogen bonding, united atom force fields and reduced representations, Force field parameterization. Potential energy surface; Convergence criteria, Optimization; multivariable optimization algorithms, minimization methods, steepest descent and conjugate gradient methods. Molecular dynamics Simulations; Newtonian dynamics; Integrators - Leapfrog and Verlet algorithms, truncated and shifted-force potentials. Implicit and explicit solvation models, periodic boundary conditions. Temperature and pressure control in molecular dynamics simulations. Conformational analysis; Evolutionary algorithms and simulated annealing, clustering and pattern recognition techniques. Monte Carlo Simulation methods; Theoretical aspects and implementation to the Metropolis method, configurationally biased Monte Carlo simulations. Methods in Drug design; Chemical databases, 2D and 3D database search, Similarity Search, Scaffold hoping, Lead identification, optimization and validation, Docking, De Novo Drug Design, Virtual screening. Quantitative structure activity relationship; Introduction to QSAR, descriptors QSARs, regression analysis and partial least squares analysis, combinatorial libraries.

 

Texts:

1.  A. R. Leach, Molecular Modeling Principles and Applications, 2nd Edition, Prentice Hall USA, 2001.

2.  T. Schlick Molecular Modeling and Simulation - An Interdisciplinary Guide, Springer verlag, 2000.

3. B. R. Donald, Algorithms in Structural Molecular Biology, Massachusetts Institute of Technology Press, 2011.

 

References:

1.  A. Hinchliffe, Molecular Modeling for Beginners, 2nd Edition, John Wiley & Sons Ltd, 2008.

2.  P. E. Bourne, Structural Bioinformtics, 2nd Edition, Wiley, 2009.

3. D. W. Mount, Bioinformatics: Sequence and Genome Analysis, 2nd Edition, CSH Press, 2005.

4.  S. G. Kochan and P. Wood, UNIX Shell Programming, 3rd Edition, SAMS, 2003.

5. P. Bultinck, Computational Medicinal Chemistry for Drug Discovery, Marcel Dekker Inc., 2004.