Week 1: Introduction: Flow of the history of biological inventions, basic Biological Macromolecules of life, i.e., Protein, Nucleic Acid, Carbohydrates & Lipid/Fat, and a comparison between polymers and "3C"ecrets of covalent bond, nucleic acid, DNA sequencing, PCR innovation, gene sequencing to genome sequencing, introduction to NGS and its different platforms, arrival of Post Genomic Era, the effect of HGP, and experimental three-dimensional structure determination techniques.
Week 2: Protein: Amino acids and their properties, Protein Chemistry, Chirality, Peptide bond, and Levels of protein structures, Dihedral angles, Peptide bond, and Ramachandran Plot, Super Secondary Structures, Motif, Domains, Non-covalent interactions, Folding of Protein, Thermodynamics, and Kinetics of protein folding, Characterization of Proteins.
Week 3: Introduction to Structural Biology Techniques: cellular organization, resolution structure determining technique with their ranges of the resolution, the success of X-ray crystallography from single molecule to a crystal, X-ray Crystallography, Crystallization in X-ray Crystallography, Crystal mounting in X-ray Crystallography.
Week 4: X-ray Crystallography: Production of X-ray and its properties, unit cell, symmetry, and lattice, the geometry of the crystal system, Crystal Symmetry, Instrumentation in X-ray Crystallography, Data collection, and processing
Week 5: X-ray Crystallography: Data Analysis of X-ray Crystallography - Diffraction Patterns, Indexing, Bragg's Law, Laue equation, Relation between "Laue equation and Bragg's Law", Lattice Transformation, Ewald Sphere, Laue Condition for Diffraction and Ewald Sphere, Structure Factors and Diffraction Pattern, Atomic Scattering Factor, Anomalous Dispersion, Analytical expression of the phase, Fourier Transformation, introduction to Phase Problem. Phase problem - Phase Problem, Patterson Function, How to solve phase problem, Heavy atom replacement methods, Isomorphous replacement, Anomalous dispersion, phase problem associated with crystal diffraction and common techniques to recover phase resolving different phase improvement methods. Refinement and Structure deposition to PDB - aspects of structure refinement, motivation, application, the procedure of simulated annealing, PDB repository, atomic model deposition as well as different PDB validation suites.
Week 6: NMR: Introduction to NMR, basic Principles of NMR and Instrumentation, NMR Sample Preparation and Chemical Shift related concepts, Factors effecting NMR Spectra (1D & 2D), 2D & 3D NMR Spectroscopy focusing on protein structure.
Week 7: Spectroscopy: Introduction to Spectroscopy, UV-Vis and CD spectroscopy, Fluorescence Spectroscopy and Green Fluorescence Protein (GFP), Infrared & Raman Spectroscopy for protein, Raman Spectroscopy, Raman Microscopy and Raman Crystallography for studying protein.
Week 8: Microscopy: Introduction to Microscopy, Functioning details of Cryo-Electron Microscopy (Cryo-EM), Cryo-Electron Microscopy: Data Collection and Analysis, A concise story of advancement Cryo-EM, Protein Data Bank.
Week 9: Molecular Visualizations: History of Molecular Visualizations of Biological Macromolecules, Description of structure-related files (.pdb, .mmcif, .mtz, etc.), Demonstration of COOT, 3D visualization using Pymol, Demonstration of Pymol.
Week 10: Molecular Dynamic Simulation: Why we need MD Simulation, Molecular Dynamic Simulation Process, Build a realistic atomistic model of the system, the algorithm behind simulation process, Concept of Topology and Parameter files, Major components in a force field, the concept of solvation, solvent models, Periodic Boundary Condition, Concept of Central Simulation Box, Phase Space, Concept of Ensembles, Energy Minimization (EM), potential energy surface (PES), Determination of EM, types of EM methods and their algorithms, Steps in MD Simulation, Application of Molecular Dynamic Simulation.
Week 11: Protein Engineering: What, How & Which of Protein Engineering, How to make logical Protein Engineering: Process of Rational design, a success story of Rational Protein designing: Focusing on De Novo Process, Designing Protein by mimicking nature: Process of Directed Evolution, Achievement, Challenges, and Future direction in the field of Protein Engineering.
Week 12: Structure-Based Drug Discovery: Introduction to Structure-Based Drug Discovery (SBDD), Rational Drug Discovery, Docking Based Virtual Screening: Progress, Challenges and Future perspective, What makes a small molecule an ideal drug: Developing in silico ADMETox Model, Structure-Based Drug Discovery: Case study and Conclusion