Lecture 45 of 60Unit 9
Demonstration of Pymol
Prof. Saugata Hazra · IIT Roorkee
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- Structural Biology, IIT Roorkee (at NPTEL)
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All the lectures
- Introduction: Why to Study Structural Biology
- Introduction to Biological Macromolecules
- Introduction: Decoding Biological Macromolecules
- Introduction: Genome Sequencing
- Introduction: Post Genomic Era
- Amino acids and their properties
- Protein: Protein Chemistry, Chirality, Peptide bond and Levels of protein structures
- Protein: Dihedral angles, Peptide bond and Ramachandran Plot
- Protein: Super Secondary Structures, Motif, Domains, Non-covalent interactions
- Protein: Folding of Protein, Thermodynamics and Kinetics of protein folding, Characterization of Proteins
- Introduction to Structural Biology Techniques Part I
- Introduction to Structural Biology Techniques Part II
- X-ray Crystallography: Crystallization Part I
- X-ray Crystallography: Crystallization Part II
- X-ray Crystallography: Crystal Mounting
- X-ray Crystallography: Production of X-ray and its properties
- X-ray Crystallography: Journey to 3D land
- X-ray Crystallography: Crystal Symmetry
- X-ray Crystallography: Instrumentation in X-ray Crystallography
- X-ray Crystallography: Data collection and processing
- X-ray Crystallography: Data Analysis Part I
- X-ray Crystallography: Data Analysis Part II
- X-ray Crystallography: Phase Problem Part I
- X-ray Crystallography: Phase Problem Part II
- X-ray Crystallography: Refinement and Structure deposition to PDB
- Introduction to Spectroscopy and 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
- 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
- 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
- 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
- Why we need MD Simulation
- Molecular Dynamic Simulation Process: Part I
- Molecular Dynamic Simulation Process: Part II
- Molecular Dynamic Simulation Process: Part III
- Application of Molecular Dynamic Simulation
- What, How & Which of Protein Engineering
- How to make logical Protein Engineering: Process of Rational design
- 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
- 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