Course

Unit 1

Introduction to Structural Biology: Structure of small molecules, Databases for small molecules, 2D and 3D structures of molecules, conversion, Draw the structures of molecules, Conversion of molecules to various formats, Databases for molecules, Chemical and physical properties of molecules, Lipinski rule, what are ADMET properties.

Unit 2

Introduction to Macromolecules: Protein database, how to understand and read 3D structure files, RCSB, reading PDB files, and related calculations, Basics of macromolecular crystallography, Introduction to importance of Nuclear Magnetic Resonance (NMR) and Cryo-Electron microscopy.

Unit 3

Introduction to Protein Sequences: screen the proteins to specific organism, compare sequences of proteins, identify the 3D structure of protein, introduction to protein-protein interactions and tools, identifying the Active sites in a protein.

Unit 4

Introduction to Ligand: Protein Interactions, concepts of Molecular Docking studies, tools for Molecular Docking, how to prepare Ligand, Protein files, importance of grid and dock files,

Unit 5

Optimization: preparation of Grid parameters and docking parameters, run the commands, validating the Autodock data, 3D visualization tools and labelling the amino acid residues.

LEARNING OBJECTIVES: 

Structural biology approaches have broadened the scope for better understanding of small molecules and macromolecules. The complete genome sequencing of an organism in days which led to generating several numbers of protein sequences and so understanding the three-dimensional structure of the protein molecules has become a necessity. The course would be helpful to students to attain good knowledge in understanding the structural aspects of biomolecules.

COURSE OUTCOMES :  

After completing the course, students shall be able to

CO1. Understand the importance of structural biology related to small molecules and their Physico-chemical properties.

CO2. Understand the 3D structure of Proteins and structural aspects of protein using bioinformatic tools.

CO3. Understand the sequence, screening, and actives sites information of the proteins.

CO4. Understand the concepts of ligand-protein interactions and molecular docking studies using Autodock.

REFERENCES: 1. Lubert Stryer, Biochemistry, 4th Edition, WH Freeman & Co. 2. Carl Ivar Branden and John Tooze., ?Introduction to Protein Structure? 2nd 2001 Edition, Taylor, and Francis.