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[ DevCourseWeb com ] Udemy - Learn Docking & Molecular Dynamics Simulation From Scratch
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01 - Important Massage Before Start of The Course
001 Important Massage from Instructors.mp4
001 Important Massage from Instructors_en.vtt
02 - (Optional) Module-1 Protein Structure Basics & Way to Get Them
001 What is Protein_.mp4
001 What is Protein__en.vtt
002 Experimental Techniques to Determine 3D Structure of Protein.mp4
002 Experimental Techniques to Determine 3D Structure of Protein_en.vtt
003 Practical-1_ How To Download Protein Structure From Protein Databank.mp4
003 Practical-1_ How To Download Protein Structure From Protein Databank_en.vtt
004 Practical-2_ Visualization of 3D Structure of Protein Using Pymol.mp4
004 Practical-2_ Visualization of 3D Structure of Protein Using Pymol_en.vtt
005 Fixing the Missing Residues in Protein 3D Structure Downloaded.mp4
005 Fixing the Missing Residues in Protein 3D Structure Downloaded_en.vtt
006 Practical-3_ Fixing Missing Residues Issue With Modeller.mp4
006 Practical-3_ Fixing Missing Residues Issue With Modeller_en.vtt
007 Intro to Protein 3D Structure Prediction.mp4
007 Intro to Protein 3D Structure Prediction_en.vtt
008 Practical-4_ How to Predict 3D Structure Using Modeller (Homology).mp4
008 Practical-4_ How to Predict 3D Structure Using Modeller (Homology)_en.vtt
009 Practical-5_ How to Use I-TASSER for Prediction of 3D Structure_.mp4
009 Practical-5_ How to Use I-TASSER for Prediction of 3D Structure__en.vtt
010 Practical-6_ Introduction of Alpha-Fold Database and Alpha-Fold Colab.mp4
010 Practical-6_ Introduction of Alpha-Fold Database and Alpha-Fold Colab_en.vtt
37081162-script1.py
37081164-script2.py
37081170-script3.py
37081186-alignmnet.ali
37727938-pdb-95.pir
37727940-qseq1.ali
37727946-script1.py
37727956-script2.py
37727968-script3.py
37727974-script4.py
37727980-script5.py
03 - Module-2_ Theory of Molecular Dynamics Simulations
001 Basic Introduction of Molecular Dynamic Simulations and its Steps.mp4
001 Basic Introduction of Molecular Dynamic Simulations and its Steps_en.vtt
002 Basic Theory of Molecular Dynamics Simulation (Part-1).mp4
002 Basic Theory of Molecular Dynamics Simulation (Part-1)_en.vtt
003 Basic Theory of Molecular Dynamics Simulation (Part-2).mp4
003 Basic Theory of Molecular Dynamics Simulation (Part-2)_en.vtt
004 Basic Theory of Molecular Dynamics Simulation (Part-3).mp4
004 Basic Theory of Molecular Dynamics Simulation (Part-3)_en.vtt
005 Basic Theory of Molecular Dynamics Simulation (Part-4).mp4
005 Basic Theory of Molecular Dynamics Simulation (Part-4)_en.vtt
006 MD (Molecular Dynamics Simulation) Cycle.mp4
006 MD (Molecular Dynamics Simulation) Cycle_en.vtt
007 Basic Steps of Molecular Dynamics Simulations.mp4
007 Basic Steps of Molecular Dynamics Simulations_en.vtt
008 Protein Structure Preparation for Molecular Dynamics Simulations.mp4
008 Protein Structure Preparation for Molecular Dynamics Simulations_en.vtt
009 Preparation of Topology File for Molecular Dynamics Simulations.mp4
009 Preparation of Topology File for Molecular Dynamics Simulations_en.vtt
010 Solvation and Ionization of System.mp4
010 Solvation and Ionization of System_en.vtt
011 Energy Minimization (EM) of System.mp4
011 Energy Minimization (EM) of System_en.vtt
012 Equilibration and Production Phase of Molecular Dynamics Simulation.mp4
012 Equilibration and Production Phase of Molecular Dynamics Simulation_en.vtt
04 - Module 3_ Computer Operating System Used for Molecular Dynamics Simulation
001 Basic Type of Operating System Available in Market.mp4
001 Basic Type of Operating System Available in Market_en.vtt
002 Features of Linux Operating System.mp4
002 Features of Linux Operating System_en.vtt
003 Terminal of Linux Operating System.mp4
003 Terminal of Linux Operating System_en.vtt
004 Some Basic Commands for Linux Operating System.mp4
004 Some Basic Commands for Linux Operating System_en.vtt
005 What's Next_.mp4
005 What's Next__en.vtt
05 - Module 4_ Demonstration of MD Simulation of Protein in Water with GROMACS
001 Practical-7 Installation of Linux in Windows Environment.mp4
001 Practical-7 Installation of Linux in Windows Environment_en.vtt
002 Practical-8 Installation of GROMACS.mp4
002 Practical-8 Installation of GROMACS_en.vtt
003 Modules of GROMACS Used in Molecular Dynamics Tutorial.mp4
003 Modules of GROMACS Used in Molecular Dynamics Tutorial_en.vtt
004 Work Flow of Molecular Dynamics in GROMACS.mp4
004 Work Flow of Molecular Dynamics in GROMACS_en.vtt
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations.mp4
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations_en.vtt
006 Commands to Run Molecular Dynamics Simulations (For You).mp4
006 Commands to Run Molecular Dynamics Simulations (For You)_en.vtt
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations.mp4
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations_en.vtt
008 Practical-11 Creation of Topology File In GROMACS.mp4
008 Practical-11 Creation of Topology File In GROMACS_en.vtt
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation.mp4
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation_en.vtt
010 Practical-13 Ionization Step in Molecular Dynamics Simulation.mp4
010 Practical-13 Ionization Step in Molecular Dynamics Simulation_en.vtt
011 Practical-14 Energy Minimization (EM) in GROMACS.mp4
011 Practical-14 Energy Minimization (EM) in GROMACS_en.vtt
012 Practical-15 Equilibration Phase-I (Part-A).mp4
012 Practical-15 Equilibration Phase-I (Part-A)_en.vtt
013 Practical-16 Equilibration Phase-I (Part-B).mp4
013 Practical-16 Equilibration Phase-I (Part-B)_en.vtt
014 Practical-17 Equilibration Phase-II (Part-A).mp4
014 Practical-17 Equilibration Phase-II (Part-A)_en.vtt
015 Practical-18 Equilibration Phase-II (Part-B).mp4
015 Practical-18 Equilibration Phase-II (Part-B)_en.vtt
016 Understanding md.mdp File Before Final Phase.mp4
016 Understanding md.mdp File Before Final Phase_en.vtt
017 Practical-19 Running Molecular Dynamics Simulation Final Phase.mp4
017 Practical-19 Running Molecular Dynamics Simulation Final Phase_en.vtt
018 Basic Theory of Molecular Dynamics Simulation Data Analysis.mp4
018 Basic Theory of Molecular Dynamics Simulation Data Analysis_en.vtt
019 Commands for Analysis of Molecular Dynamics Simulation Data.mp4
019 Commands for Analysis of Molecular Dynamics Simulation Data_en.vtt
020 Bringing the Protein in Center Before Data Analysis.mp4
020 Bringing the Protein in Center Before Data Analysis_en.vtt
021 Practical-20 Calculation of RMSD.mp4
021 Practical-20 Calculation of RMSD_en.vtt
022 Practical-21 Calculation of RMSF.mp4
022 Practical-21 Calculation of RMSF_en.vtt
023 Practical-22 Calculation of Radius of Gyration (Rg).mp4
023 Practical-22 Calculation of Radius of Gyration (Rg)_en.vtt
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb).mp4
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)_en.vtt
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA).mp4
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)_en.vtt
026 Practical-25 Opening of XVG Files in Excel.mp4
026 Practical-25 Opening of XVG Files in Excel_en.vtt
027 Practical-25.1_ Visualization of MD Trajectory in Pymol.mp4
027 Practical-25.1_ Visualization of MD Trajectory in Pymol_en.vtt
37706258-Commands-to-Install-GROMACS-Using-Linux-Terminal.pdf
37706644-Commands-to-run-MD-simulation-of-Protein-in-Water.pdf
37706684-ions.mdp
37706700-minim.mdp
37706750-nvt.mdp
37706768-npt.mdp
37707482-md.mdp
37707724-Commands-to-Analyze-the-MD-Data.pdf
06 - Module-5_ Fundamentals of Molecular Docking (Theory & Practical)
001 Introduction of Docking-Part-1.mp4
001 Introduction of Docking-Part-1_en.vtt
002 Introduction of Docking-Part-2.mp4
002 Introduction of Docking-Part-2_en.vtt
003 Sampling Algorithms-Part-1.mp4
003 Sampling Algorithms-Part-1_en.vtt
004 Sampling Algorithms-Part-2.mp4
004 Sampling Algorithms-Part-2_en.vtt
005 Sampling Algorithms-Part-3.mp4
005 Sampling Algorithms-Part-3_en.vtt
006 Sampling Algorithms-Part-4.mp4
006 Sampling Algorithms-Part-4_en.vtt
007 Scoring Algorithms.mp4
007 Scoring Algorithms_en.vtt
008 Types of Docking.mp4
008 Types of Docking_en.vtt
009 Basic Steps in Docking Protocol.mp4
009 Basic Steps in Docking Protocol_en.vtt
010 Theory of Docking Steps-Part-1.mp4
010 Theory of Docking Steps-Part-1_en.vtt
011 Theory of Docking Steps-Part-2.mp4
011 Theory of Docking Steps-Part-2_en.vtt
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid.mp4
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid_en.vtt
013 Practical-27_ Installation of Ligand Drawing Tools.mp4
013 Practical-27_ Installation of Ligand Drawing Tools_en.vtt
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking.mp4
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking_en.vtt
015 Issue With Protein Structure Preparation in MGL Tools.mp4
015 Issue With Protein Structure Preparation in MGL Tools_en.vtt
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database.mp4
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database_en.vtt
017 Practical-30 Drawing of Ligand Structure in ChemSketch.mp4
017 Practical-30 Drawing of Ligand Structure in ChemSketch_en.vtt
018 Practical-31 Preparation of Ligand Molecule for Docking.mp4
018 Practical-31 Preparation of Ligand Molecule for Docking_en.vtt
019 Practical-32 Prediction of Active Site of Protein.mp4
019 Practical-32 Prediction of Active Site of Protein_en.vtt
020 Practical-33 Setting Grid.mp4
020 Practical-33 Setting Grid_en.vtt
021 Very Important Step; Be Careful Here.mp4
021 Very Important Step; Be Careful Here_en.vtt
022 Practical-34 (Part-A) Performing Docking with Vina.mp4
022 Practical-34 (Part-A) Performing Docking with Vina_en.vtt
023 Practical-34 (Part-B) Visualization of Vina Docking Data.mp4
023 Practical-34 (Part-B) Visualization of Vina Docking Data_en.vtt
024 Practical-35 (Part-A) Performing Docking Using AutoDock4.mp4
024 Practical-35 (Part-A) Performing Docking Using AutoDock4_en.vtt
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results.mp4
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results_en.vtt
026 Practical-33 Preforming Docking with CB Dock.mp4
026 Practical-33 Preforming Docking with CB Dock_en.vtt
027 Practical-34 Analyzing the Docking Data.mp4
027 Practical-34 Analyzing the Docking Data_en.vtt
028 Practical-35_ PatchDock; Shape Complementary Docking Program.mp4
028 Practical-35_ PatchDock; Shape Complementary Docking Program_en.vtt
37707734-conf.txt
07 - Module-6_ Molecular Dynamics Simulations of Protein-Ligand Docked Complex
001 Biggest Drawback of Conventional Docking Protocol.mp4
001 Biggest Drawback of Conventional Docking Protocol_en.vtt
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations.mp4
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations_en.vtt
003 Basic Steps of Protein-Ligand MD Simulations.mp4
003 Basic Steps of Protein-Ligand MD Simulations_en.vtt
004 Practical-36_ Very First Step; Preparation of Protein and Ligand.mp4
004 Practical-36_ Very First Step; Preparation of Protein and Ligand_en.vtt
005 Practical-37_ Necessary Files Needed For Molecular Dynamics Simulations.mp4
005 Practical-37_ Necessary Files Needed For Molecular Dynamics Simulations_en.vtt
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations.mp4
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations_en.vtt
007 Practical-38_ Preparation of Protein Topology File.mp4
007 Practical-38_ Preparation of Protein Topology File_en.vtt
008 Practical-39_ Preparation of Ligand Topology File.mp4
008 Practical-39_ Preparation of Ligand Topology File_en.vtt
009 Practical-40_ Making Complex.mp4
009 Practical-40_ Making Complex_en.vtt
010 Practical-41_ Solvation, Ionization & Energy Minimization of Complex.mp4
010 Practical-41_ Solvation, Ionization & Energy Minimization of Complex_en.vtt
011 Practical-42_ Ligand Restrain.mp4
011 Practical-42_ Ligand Restrain_en.vtt
012 Practical-43_ Thermostats.mp4
012 Practical-43_ Thermostats_en.vtt
013 Practical-44_ Equilibration.mp4
013 Practical-44_ Equilibration_en.vtt
014 Practical-44_ Production Phase.mp4
014 Practical-44_ Production Phase_en.vtt
015 Practical-44_ Analysis.mp4
015 Practical-44_ Analysis_en.vtt
37390682-cgenff-charmm2gmx.py
37390690-sort-mol2-bonds.pl
37390692-em.mdp
37390700-ie.mdp
37390704-ions.mdp
37390714-md.mdp
37390722-npt.mdp
37390728-nvt.mdp
37708482-Commands-for-MD-Ligand-Protein-Complex.pdf
37708606-Commands-to-Analyze-the-Molecular-Dynamics-Simulation-Data-of-Ligand-Protein-Complex.pdf
08 - Module-7_ Virtual Screening of Drugs
001 Importance of Virtual Screening.mp4
001 Importance of Virtual Screening_en.vtt
002 Introduction to Virtual Screening.mp4
002 Introduction to Virtual Screening_en.vtt
003 Fundamental Steps of Virtual Screening.mp4
003 Fundamental Steps of Virtual Screening_en.vtt
004 Commands Needed to Run Virtual Screening.mp4
004 Commands Needed to Run Virtual Screening_en.vtt
005 Practical-46_ Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu).mp4
005 Practical-46_ Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)_en.vtt
006 Practical-47_ Preparation of Protein Receptor for Virtual Screening.mp4
006 Practical-47_ Preparation of Protein Receptor for Virtual Screening_en.vtt
007 Practical-48_ Downloading of Thousands of Ligands in One Click.mp4
007 Practical-48_ Downloading of Thousands of Ligands in One Click_en.vtt
008 Practical-49_ Preparation of Ligands for Docking.mp4
008 Practical-49_ Preparation of Ligands for Docking_en.vtt
009 Practical-50_ Setting Grid and Writing of Configuration File.mp4
009 Practical-50_ Setting Grid and Writing of Configuration File_en.vtt
010 Practical-51_ Docking of Ligands with Receptors in Vina.mp4
010 Practical-51_ Docking of Ligands with Receptors in Vina_en.vtt
011 Practical-52_ Analysis.mp4
011 Practical-52_ Analysis_en.vtt
37709016-Vina-linux.pl
37713454-Commands-to-Run-Vina-for-Virtual-Screening-in-Linux-Environment.pdf
Bonus Resources.txt
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