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, 2^nd 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, 2^nd Edition, John Wiley & Sons Ltd, 2008.

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

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

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

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