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    • Learn Docking and Molecular Dynamics Simulation from Scratch

    Learn Docking & Molecular Dynamics Simulation From Scratch

    BY
    Udemy

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    Mode

    Online

    Fees

    ₹ 3199

    Quick Facts

    particular details
    Medium of instructions English
    Mode of learning Self study
    Mode of Delivery Video and Text Based

    Course and certificate fees

    Fees information
    ₹ 3,199
    certificate availability

    Yes

    certificate providing authority

    Udemy

    The syllabus

    Important Massage Before Start of The Course

    • Important Massage from Instructors

    (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

    Dr Muhammad Dujana
    Instructor
    Freelancer

    Ph.D

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