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Important Massage from Instructors
Quick Facts
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Medium of instructions
English
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Mode of learning
Self study
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Mode of Delivery
Video and Text Based
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Course and certificate fees
Fees information
₹ 3,199
certificate availability
Yes
certificate providing authority
Udemy
The syllabus
Important Massage Before Start of The Course
(Optional) Module-1 Protein Structure Basics & Way to Get Them
- What is Protein?
- Experimental Techniques to Determine 3D Structure of Protein
- Practical-1: How To Download Protein Structure From Protein Databank
- Practical-2: Visualization of 3D Structure of Protein Using Pymol
- Fixing the Missing Residues in Protein 3D Structure Downloaded
- Practical-3: Fixing Missing Residues Issue With Modeller
- Intro to Protein 3D Structure Prediction
- Practical-4: How to Predict 3D Structure Using Modeller (Homology)
- Practical-5: How to Use I-TASSER for Prediction of 3D Structure?
- Practical-6: Introduction of Alpha-Fold Database and Alpha-Fold Colab
- Quiz 1: Knowledge Check of Module-1
- Assignment-1: Fix the Missing Amino Acids Residues in the Protein Structure
Module-2: Theory of Molecular Dynamics Simulations
- Basic Introduction of Molecular Dynamic Simulations and its Steps
- Basic Theory of Molecular Dynamics Simulation (Part-1)
- Basic Theory of Molecular Dynamics Simulation (Part-2)
- Basic Theory of Molecular Dynamics Simulation (Part-3)
- Basic Theory of Molecular Dynamics Simulation (Part-4)
- MD (Molecular Dynamics Simulation) Cycle
- Basic Steps of Molecular Dynamics Simulations
- Protein Structure Preparation for Molecular Dynamics Simulations
- Preparation of Topology File for Molecular Dynamics Simulations
- Solvation and Ionization of System
- Energy Minimization (EM) of System
- Equilibration and Production Phase of Molecular Dynamics Simulation
- Quiz 2: Knowledge Check of Module 2
Module 3: Computer Operating System Used for Molecular Dynamics Simulation
- Basic Type of Operating System Available in Market
- Features of Linux Operating System
- Terminal of Linux Operating System
- Some Basic Commands for Linux Operating System
- What's Next?
- Quiz 3: Knowledge Check of Module-3
Module 4: Demonstration of MD Simulation of Protein in Water with GROMACS
- Practical-7 Installation of Linux in Windows Environment
- Practical-8 Installation of GROMACS
- Modules of GROMACS Used in Molecular Dynamics Tutorial
- Work Flow of Molecular Dynamics in GROMACS
- Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations
- Commands to Run Molecular Dynamics Simulations (For You)
- Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations
- Practical-11 Creation of Topology File In GROMACS
- Practical-12 Solvation of Step in Molecular Dynamics Simulation
- Practical-13 Ionization Step in Molecular Dynamics Simulation
- Practical-14 Energy Minimization (EM) in GROMACS
- Practical-15 Equilibration Phase-I (Part-A)
- Practical-16 Equilibration Phase-I (Part-B)
- Practical-17 Equilibration Phase-II (Part-A)
- Practical-18 Equilibration Phase-II (Part-B)
- Understanding md.mdp File Before Final Phase
- Practical-19 Running Molecular Dynamics Simulation Final Phase
- Basic Theory of Molecular Dynamics Simulation Data Analysis
- Commands for Analysis of Molecular Dynamics Simulation Data
- Bringing the Protein in Center Before Data Analysis
- Practical-20 Calculation of RMSD
- Practical-21 Calculation of RMSF
- Practical-22 Calculation of Radius of Gyration (Rg)
- Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)
- Practical-24 Calculation of Solvent Accessible Surface Area (SASA)
- Practical-25 Opening of XVG Files in Excel
- Practical-25.1: Visualization of MD Trajectory in Pymol
- Quiz 4: Knowledge Check of Module 4
Module-5: Fundamentals of Molecular Docking (Theory & Practical)
- Introduction of Docking-Part-1
- Introduction of Docking-Part-2
- Sampling Algorithms-Part-1
- Sampling Algorithms-Part-2
- Sampling Algorithms-Part-3
- Sampling Algorithms-Part-4
- Scoring Algorithms
- Types of Docking
- Basic Steps in Docking Protocol
- Theory of Docking Steps-Part-1
- Theory of Docking Steps-Part-2
- Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid
- Practical-27: Installation of Ligand Drawing Tools
- Practical-28 Downloading and Preparation of Protein 3D Structure for Docking
- Issue With Protein Structure Preparation in MGL Tools
- Practical-29 Downloading of Ligand 3D Structure from ZINC Database
- Practical-30 Drawing of Ligand Structure in ChemSketch
- Practical-31 Preparation of Ligand Molecule for Docking
- Practical-32 Prediction of Active Site of Protein
- Practical-33 Setting Grid
- Very Important Step; Be Careful Here
- Practical-34 (Part-A) Performing Docking with Vina
- Practical-34 (Part-B) Visualization of Vina Docking Data
- Practical-35 (Part-A) Performing Docking Using AutoDock4
- Practical-35 (Part-B) Visualization of AutoDock4 Docking Results
- Practical-33 Preforming Docking with CB Dock
- Practical-34 Analyzing the Docking Data
- Practical-35: PatchDock; Shape Complementary Docking Program
- Quiz 5: Knowledge Check of Module 5
Module-6: Molecular Dynamics Simulations of Protein-Ligand Docked Complex
- Biggest Drawback of Conventional Docking Protocol
- Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations
- Basic Steps of Protein-Ligand MD Simulations
- Practical-36: Very First Step; Preparation of Protein and Ligand
- Practical-37: Necessary Files Needed For Molecular Dynamics Simulations
- Commands to Run Ligand-Protein Molecular Dynamics Simulations
- Practical-38: Preparation of Protein Topology File
- Practical-39: Preparation of Ligand Topology File
- Practical-40: Making Complex
- Practical-41: Solvation, Ionization & Energy Minimization of Complex
- Practical-42: Ligand Restrain
- Practical-43: Thermostats
- Practical-44: Equilibration
- Practical-44: Production Phase
- Practical-44: Analysis
Module-7: Virtual Screening of Drugs
- Importance of Virtual Screening
- Introduction to Virtual Screening
- Fundamental Steps of Virtual Screening
- Commands Needed to Run Virtual Screening
- Practical-46: Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)
- Practical-47: Preparation of Protein Receptor for Virtual Screening
- Practical-48: Downloading of Thousands of Ligands in One Click
- Practical-49: Preparation of Ligands for Docking
- Practical-50: Setting Grid and Writing of Configuration File
- Practical-51: Docking of Ligands with Receptors in Vina
- Practical-52: Analysis
Instructors
Dr Muhammad Dujana
Instructor
Freelancer
Ph.D
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