Learn Docking & Molecular Dynamics Simulation From Scratch

BY
Udemy

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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