Currently, there is high use of bioinformatics tools in biological studies. This Advance Bioinformatics course includes theory and practical aspects of molecular docking and molecular dynamics simulation for you. In this course, we have tried to explain the theory and practical steps which are required to perform the above-mentioned bioinformatics techniques. We strongly believe that after having this course, you will be well versed in ligand-protein docking and molecular dynamics simulations.
This course is designed to keep the need of biologists in view. We tried to explain every step in a simple and elegant way. Like our previous course, “Learn Bioinformatics From Scratch (Theory & Practical)” in this course, we took start from scratch. So, if you are new in this field then it will be easy for you to move with the flow. There is a total of seven modules with 104 lectures. In this course, you will learn
(1) Protein Structural Bioinformatics
(2) Theory of Molecular Dynamics Simulation
(3) Introduction of Linux Environment
(4) Practical Demonstration of Protein Molecular Dynamics Simulation
(5) Ligand-Protein Docking (Theory & Practical)
(6) Practical Demonstration of Ligand-Protein Complex Molecular Dynamics Simulation
(7) Virtual Screening of Ligands with Protein Using Vina
This course is a unique blend of theory and practical. We assure you that after having this course, performing molecular docking and molecular dynamics will be easy for you. We have used open-source software in this course so that you do not need to purchase any expensive software. The tools which are demonstrated in this course are Modeller, I-TASSER, Alpha-Fold (Colab), Auto-dock4, Vina, Patch-Dock, GROMACS, LigPlot, ChemSketch, OpenBabel, Pymol, and a lot more. These tools are freely available and closely related to the course material, and students will need to sign up for some tools to access it.
So what are you waiting for? Click the enroll button and start this amazing journey. We hope that the content of this course will be worth your money. We assure every possible assistance throughout your learning process. We always respond to Questions and Queries which you will forward to us. We believe that we will grow with you.
Your growth is our growth.
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2
What is Protein? -
3
Experimental Techniques to Determine 3D Structure of Protein
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4
Practical-1: How To Download Protein Structure From Protein Databank
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Practical-2: Visualization of 3D Structure of Protein Using Pymol
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Fixing the Missing Residues in Protein 3D Structure Downloaded
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Practical-3: Fixing Missing Residues Issue With Modeller
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Intro to Protein 3D Structure Prediction
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Practical-4: How to Predict 3D Structure Using Modeller (Homology)
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Assignment 2 -
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Practical-5: How to Use I-TASSER for Prediction of 3D Structure?
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Practical-6: Introduction of Alpha-Fold Database and Alpha-Fold Colab
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Assignment 3
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Quiz 1: Knowledge Check of Module-1In this quiz, you will check your knowledge of module-1. Good luck with the quiz.
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Assignment-1: Fix the Missing Amino Acids Residues in the Protein Structure
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Basic Introduction of Molecular Dynamic Simulations and its Steps
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Basic Theory of Molecular Dynamics Simulation (Part-1)
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Basic Theory of Molecular Dynamics Simulation (Part-2)
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Basic Theory of Molecular Dynamics Simulation (Part-3)
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Basic Theory of Molecular Dynamics Simulation (Part-4)
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MD (Molecular Dynamics Simulation) Cycle
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Basic Steps of Molecular Dynamics Simulations
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Protein Structure Preparation for Molecular Dynamics Simulations
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Preparation of Topology File for Molecular Dynamics Simulations
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Solvation and Ionization of System
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Energy Minimization (EM) of System
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Equilibration and Production Phase of Molecular Dynamics Simulation
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Quiz 2: Knowledge Check of Module 2
In this quiz, you will check your knowledge of module-2. Good luck with the quiz.
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Basic Type of Operating System Available in Market
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Features of Linux Operating System
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Terminal of Linux Operating System
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Some Basic Commands for Linux Operating System
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What's Next?
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Quiz 3: Knowledge Check of Module-3
In this quiz, you will check your knowledge of module-3. Good luck with the quiz.
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Practical-7 Installation of Linux in Windows Environment
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Practical-8 Installation of GROMACS
Sometimes, the link that we have provided to you for the installation of GROMACS may be broken. In this case, please do not worry. Please let us tell you the other way to install the GROMACS
Step-1:
Please download the text file from the Resource section of the video. The file contains all of the necessary links and commands to install the GROMACS.
Using the Google Drive Link present in the text file that you have just downloaded, download the gromacs_install.sh file.
Step -2:
Once you download the file please move to the folder where you downloaded the above file. For instance, if you have downloaded the file in your D drive, then please move it to the D drive. How can you move to D Drive? Please use the following set of commands to move to your D drive:
Note: We are assuming that you are using WSL (Linux environment) in Windows. If you are using the full Linux operating system (Ubuntu) then there is no need to use the first command
cd /mnt
cd d
sudo apt update
sudo apt upgrade
Note: In case you are using the full Ubuntu operating system then you can move to the folder directly. Let's assume that you have downloaded the file in the Download folder then you can use cd Downloads
Now please use the following commands to run the file that you have downloaded
sudo chmod +x gromacs_install.sh
./gromacs_install.sh
We hope this time you will not face any issues in the installation of GROMACS. In case of any further issues, please do not hesitate to contact us.
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Modules of GROMACS Used in Molecular Dynamics Tutorial
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Work Flow of Molecular Dynamics in GROMACS
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Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations
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Commands to Run Molecular Dynamics Simulations (For You)
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Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations
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Practical-11 Creation of Topology File In GROMACS
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Practical-12 Solvation of Step in Molecular Dynamics Simulation
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Practical-13 Ionization Step in Molecular Dynamics Simulation
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Practical-14 Energy Minimization (EM) in GROMACS
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Practical-15 Equilibration Phase-I (Part-A)
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Practical-16 Equilibration Phase-I (Part-B)
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Practical-17 Equilibration Phase-II (Part-A)
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Practical-18 Equilibration Phase-II (Part-B)
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Understanding md.mdp File Before Final Phase
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Practical-19 Running Molecular Dynamics Simulation Final Phase
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Basic Theory of Molecular Dynamics Simulation Data Analysis
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Commands for Analysis of Molecular Dynamics Simulation Data
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Bringing the Protein in Center Before Data Analysis
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Practical-20 Calculation of RMSD
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Practical-21 Calculation of RMSF
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Practical-22 Calculation of Radius of Gyration (Rg)
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Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)
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Practical-24 Calculation of Solvent Accessible Surface Area (SASA)
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Assignment4: Sample MD XTC file for Practice
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Practical-25 Opening of XVG Files in Excel
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Practical-25.1: Visualization of MD Trajectory in Pymol
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Quiz 4: Knowledge Check of Module 4
In this quiz, you will check your knowledge of module-4. Good luck with the quiz.
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Introduction of Docking-Part-1
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Introduction of Docking-Part-2
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Sampling Algorithms-Part-1
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Sampling Algorithms-Part-2
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Sampling Algorithms-Part-3
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Sampling Algorithms-Part-4
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Scoring Algorithms
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Types of Docking
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Basic Steps in Docking Protocol
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Theory of Docking Steps-Part-1
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Theory of Docking Steps-Part-2
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Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid
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Practical-27: Installation of Ligand Drawing Tools
The OpenBabel Website is down nowadays. If you are finding issue with the Openbabel Website then please do not worry. We have added another link in the resoruce file for you to download Openbabel for windows.
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Practical-28 Downloading and Preparation of Protein 3D Structure for Docking
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Issue With Protein Structure Preparation in MGL Tools
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Practical-29 Downloading of Ligand 3D Structure from ZINC Database
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Practical-30 Drawing of Ligand Structure in ChemSketch
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Practical-31 Preparation of Ligand Molecule for Docking
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Practical-32 Prediction of Active Site of Protein
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Practical-33 Setting Grid
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Very Important Step; Be Careful Here
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Practical-34 (Part-A) Performing Docking with Vina
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Practical-34 (Part-B) Visualization of Vina Docking Data
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Practical-35 (Part-A) Performing Docking Using AutoDock4
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Practical-35 (Part-B) Visualization of AutoDock4 Docking Results
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Practical-33 Preforming Docking with CB Dock
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Practical-34 Analyzing the Docking Data
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Practical-34(A) Performing AutoDock Vina Docking Using SwissDock
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Practical-35: PatchDock; Shape Complementary Docking Program
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Quiz 5: Knowledge Check of Module 5
In this quiz, you will check your knowledge of module-5. Good luck with the quiz.
