Syllabus of Jawaharlal Nehru University MSc Biotechnology - BT531 - Computational Biology-II

Credits: 2

Introduction to Molecular Structures:

Concept of external and internal coordinates and algorithms for their interconversion. Different representations of molecular structures and their relative merits and demerits.

Experimental Methods for Molecular Structure Determination:

Brief account of structure determination by X-ray crystallography and NMR spectroscopy. Validation of experimentally obtained NMR structures. The Protein Data Bank (PDB) and the Nucleic Acid Data Bank (NDB). The PDB and the mmCIF file formats for the storage and dissemination of molecular structures.

Conformational Analysis:

Concept of free energy of molecules. Introduction to various force fields and their relative merits and demerits. Techniques for Molecular energy minimization, Monte Carlo and Molecular Dynamics simulation.

Molecular Modelling:

Methods of molecular modeling including homology modeling, threading and ab initio protein structure prediction together with their relative merits and demerits. Methods for structure-structure comparison of macromolecules with special reference to proteins.

Drug Design:

General ideas of drug designing, 2D and 3D QASR, concept of a pharmacophore and pharmacophore based searches of ligand databases. Concepts of COMFA. Methods for simulated docking.