Bioinformatics Learn Docking Mol Dynamics Simulation

Best Bioinformatics Course To Learn Advance Bioinformatics Techniques Like Docking & Molecular Dynamics Simulations
Bioinformatics Learn Docking Mol Dynamics Simulation
File Size :
4.09 GB
Total length :
7h 58m



Muhammad Dujana


Last update




Bioinformatics Learn Docking Mol Dynamics Simulation

What you’ll learn

You will learn basics of Structural Bioinformatics Including Protein Structure Prediction
You will learn Basic Theory of Molecular Dynamics Simulations and Docking
You will Get Basic Introduction of Linux Operating Systems and Its Commands
You will have Practical Demonstration of Protein Molecular Dynamics Simulations in GROMACS
You will Learn Analysis of MD Trajectory Including RMSD, RMSF, Radius of Gyration, Solvent Accessible Surface Area, Total Number of Hydrogen Bonds etc
You will have Practical Demonstration of AutoDock, Vina, CB-Dock and PatchDock for Ligand Protein Docking
You will have Practical Demonstration of MD Simulation of Ligand-Protein Complex in GROMACS
You will Learn about Virtual Screening of Drugs (Theory and Practical)

Bioinformatics Learn Docking Mol Dynamics Simulation


In online teaching, it’s always hard to engage the students. Therefore we have designed this course keeping the psychology of students in view. Usually, students start to lose their interest when they are stuck in a complex concept that’s why We tried to move from simple to complex easily and understandably.
You need to be familiar with very basics of protein structures. This will be more then enough for you to take start of this course. We have tried our level best to take start from scratch in every module by assuming it that our students know nothing.
Although, its not mandatory but we will encourage you to take our course “Learn Bioinformatics From Scratch (Theory and Practical)” on udemy. This course may also help you to grab the concepts in better way.


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 VinaThis 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. 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.


Section 1: Important Massage Before Start of The Course

Lecture 1 Important Massage from Instructors

Section 2: (Optional) Module-1 Protein Structure Basics & Way to Get Them

Lecture 2 What is Protein?

Lecture 3 Experimental Techniques to Determine 3D Structure of Protein

Lecture 4 Practical-1: How To Download Protein Structure From Protein Databank

Lecture 5 Practical-2: Visualization of 3D Structure of Protein Using Pymol

Lecture 6 Fixing the Missing Residues in Protein 3D Structure Downloaded

Lecture 7 Practical-3: Fixing Missing Residues Issue With Modeller

Lecture 8 Intro to Protein 3D Structure Prediction

Lecture 9 Practical-4: How to Predict 3D Structure Using Modeller (Homology)

Lecture 10 Practical-5: How to Use I-TASSER for Prediction of 3D Structure?

Lecture 11 Practical-6: Introduction of Alpha-Fold Database and Alpha-Fold Colab

Section 3: Module-2: Theory of Molecular Dynamics Simulations

Lecture 12 Basic Introduction of Molecular Dynamic Simulations and its Steps

Lecture 13 Basic Theory of Molecular Dynamics Simulation (Part-1)

Lecture 14 Basic Theory of Molecular Dynamics Simulation (Part-2)

Lecture 15 Basic Theory of Molecular Dynamics Simulation (Part-3)

Lecture 16 Basic Theory of Molecular Dynamics Simulation (Part-4)

Lecture 17 MD (Molecular Dynamics Simulation) Cycle

Lecture 18 Basic Steps of Molecular Dynamics Simulations

Lecture 19 Protein Structure Preparation for Molecular Dynamics Simulations

Lecture 20 Preparation of Topology File for Molecular Dynamics Simulations

Lecture 21 Solvation and Ionization of System

Lecture 22 Energy Minimization (EM) of System

Lecture 23 Equilibration and Production Phase of Molecular Dynamics Simulation

Section 4: Module 3: Computer Operating System Used for Molecular Dynamics Simulation

Lecture 24 Basic Type of Operating System Available in Market

Lecture 25 Features of Linux Operating System

Lecture 26 Terminal of Linux Operating System

Lecture 27 Some Basic Commands for Linux Operating System

Lecture 28 What’s Next?

Section 5: Module 4: Demonstration of MD Simulation of Protein in Water with GROMACS

Lecture 29 Practical-7 Installation of Linux in Windows Environment

Lecture 30 Practical-8 Installation of GROMACS

Lecture 31 Modules of GROMACS Used in Molecular Dynamics Tutorial

Lecture 32 Work Flow of Molecular Dynamics in GROMACS

Lecture 33 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations

Lecture 34 Commands to Run Molecular Dynamics Simulations (For You)

Lecture 35 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations

Lecture 36 Practical-11 Creation of Topology File In GROMACS

Lecture 37 Practical-12 Solvation of Step in Molecular Dynamics Simulation

Lecture 38 Practical-13 Ionization Step in Molecular Dynamics Simulation

Lecture 39 Practical-14 Energy Minimization (EM) in GROMACS

Lecture 40 Practical-15 Equilibration Phase-I (Part-A)

Lecture 41 Practical-16 Equilibration Phase-I (Part-B)

Lecture 42 Practical-17 Equilibration Phase-II (Part-A)

Lecture 43 Practical-18 Equilibration Phase-II (Part-B)

Lecture 44 Understanding md.mdp File Before Final Phase

Lecture 45 Practical-19 Running Molecular Dynamics Simulation Final Phase

Lecture 46 Basic Theory of Molecular Dynamics Simulation Data Analysis

Lecture 47 Commands for Analysis of Molecular Dynamics Simulation Data

Lecture 48 Bringing the Protein in Center Before Data Analysis

Lecture 49 Practical-20 Calculation of RMSD

Lecture 50 Practical-21 Calculation of RMSF

Lecture 51 Practical-22 Calculation of Radius of Gyration (Rg)

Lecture 52 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)

Lecture 53 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)

Lecture 54 Practical-25 Opening of XVG Files in Excel

Lecture 55 Practical-25.1: Visualization of MD Trajectory in Pymol

Section 6: Module-5: Fundamentals of Molecular Docking (Theory & Practical)

Lecture 56 Introduction of Docking-Part-1

Lecture 57 Introduction of Docking-Part-2

Lecture 58 Sampling Algorithms-Part-1

Lecture 59 Sampling Algorithms-Part-2

Lecture 60 Sampling Algorithms-Part-3

Lecture 61 Sampling Algorithms-Part-4

Lecture 62 Scoring Algorithms

Lecture 63 Types of Docking

Lecture 64 Basic Steps in Docking Protocol

Lecture 65 Theory of Docking Steps-Part-1

Lecture 66 Theory of Docking Steps-Part-2

Lecture 67 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid

Lecture 68 Practical-27: Installation of Ligand Drawing Tools

Lecture 69 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking

Lecture 70 Issue With Protein Structure Preparation in MGL Tools

Lecture 71 Practical-29 Downloading of Ligand 3D Structure from ZINC Database

Lecture 72 Practical-30 Drawing of Ligand Structure in ChemSketch

Lecture 73 Practical-31 Preparation of Ligand Molecule for Docking

Lecture 74 Practical-32 Prediction of Active Site of Protein

Lecture 75 Practical-33 Setting Grid

Lecture 76 Very Important Step; Be Careful Here

Lecture 77 Practical-34 (Part-A) Performing Docking with Vina

Lecture 78 Practical-34 (Part-B) Visualization of Vina Docking Data

Lecture 79 Practical-35 (Part-A) Performing Docking Using AutoDock4

Lecture 80 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results

Lecture 81 Practical-33 Preforming Docking with CB Dock

Lecture 82 Practical-34 Analyzing the Docking Data

Lecture 83 Practical-35: PatchDock; Shape Complementary Docking Program

Section 7: Module-6: Molecular Dynamics Simulations of Protein-Ligand Docked Complex

Lecture 84 Biggest Drawback of Conventional Docking Protocol

Lecture 85 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations

Lecture 86 Basic Steps of Protein-Ligand MD Simulations

Lecture 87 Practical-36: Very First Step; Preparation of Protein and Ligand

Lecture 88 Practical-37: Necessary Files Needed For Molecular Dynamics Simulations

Lecture 89 Commands to Run Ligand-Protein Molecular Dynamics Simulations

Lecture 90 Practical-38: Preparation of Protein Topology File

Lecture 91 Practical-39: Preparation of Ligand Topology File

Lecture 92 Practical-40: Making Complex

Lecture 93 Practical-41: Solvation, Ionization & Energy Minimization of Complex

Lecture 94 Practical-42: Ligand Restrain

Lecture 95 Practical-43: Thermostats

Lecture 96 Practical-44: Equilibration

Lecture 97 Practical-44: Production Phase

Lecture 98 Practical-44: Analysis

Section 8: Module-7: Virtual Screening of Drugs

Lecture 99 Importance of Virtual Screening

Lecture 100 Introduction to Virtual Screening

Lecture 101 Fundamental Steps of Virtual Screening

Lecture 102 Commands Needed to Run Virtual Screening

Lecture 103 Practical-46: Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)

Lecture 104 Practical-47: Preparation of Protein Receptor for Virtual Screening

Lecture 105 Practical-48: Downloading of Thousands of Ligands in One Click

Lecture 106 Practical-49: Preparation of Ligands for Docking

Lecture 107 Practical-50: Setting Grid and Writing of Configuration File

Lecture 108 Practical-51: Docking of Ligands with Receptors in Vina

Lecture 109 Practical-52: Analysis

Section 9: Recent Updates in Structural Biology For MD and Docking

Lecture 110 Protein Databank Update

Lecture 111 How to make Good Publication Quality Images in Pymol?

Lecture 112 Analysis of Docking Data Using LigPlot+

This course is for those who are interested to drug discovery.,This course is also suitable for those who want to be protein engineers and interested in denovo protein design.

Course Information:

Udemy | English | 7h 58m | 4.09 GB
Created by: Muhammad Dujana

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