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[ DevCourseWeb com ] Udemy - Bioinformatics; Learn Docking and Mol Dynamics Simulation
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01 - Important Massage Before Start of The Course
001 Important Massage from Instructors.mp4
001 Important Massage from Instructors_en.srt
02 - (Optional) Module-1 Protein Structure Basics & Way to Get Them
001 What is Protein.mp4
001 What is Protein_en.srt
002 Experimental Techniques to Determine 3D Structure of Protein.mp4
002 Experimental Techniques to Determine 3D Structure of Protein_en.srt
003 Practical-1 How To Download Protein Structure From Protein Databank.mp4
003 Practical-1 How To Download Protein Structure From Protein Databank_en.srt
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol.mp4
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol_en.srt
005 Fixing the Missing Residues in Protein 3D Structure Downloaded.mp4
005 Fixing the Missing Residues in Protein 3D Structure Downloaded_en.srt
006 Practical-3 Fixing Missing Residues Issue With Modeller.mp4
006 Practical-3 Fixing Missing Residues Issue With Modeller_en.srt
006 alignment.ali
006 script1.py
006 script2.py
006 script3.py
007 Intro to Protein 3D Structure Prediction.mp4
007 Intro to Protein 3D Structure Prediction_en.srt
008 Modeller-access-in-MAC.mp4
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology).mp4
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology)_en.srt
008 pdb-95.pir
008 qseq1.ali
008 script1.py
008 script2.py
008 script3.py
008 script4.py
008 script5.py
008 tseq1.pdb
008 tseq2.pdb
008 tseq3.pdb
008 tseq4.pdb
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.srt
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.srt
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.srt
002 Basic Theory of Molecular Dynamics Simulation (Part-1).mp4
002 Basic Theory of Molecular Dynamics Simulation (Part-1)_en.srt
003 Basic Theory of Molecular Dynamics Simulation (Part-2).mp4
003 Basic Theory of Molecular Dynamics Simulation (Part-2)_en.srt
004 Basic Theory of Molecular Dynamics Simulation (Part-3).mp4
004 Basic Theory of Molecular Dynamics Simulation (Part-3)_en.srt
005 Basic Theory of Molecular Dynamics Simulation (Part-4).mp4
005 Basic Theory of Molecular Dynamics Simulation (Part-4)_en.srt
006 MD (Molecular Dynamics Simulation) Cycle.mp4
006 MD (Molecular Dynamics Simulation) Cycle_en.srt
007 Basic Steps of Molecular Dynamics Simulations.mp4
007 Basic Steps of Molecular Dynamics Simulations_en.srt
008 Protein Structure Preparation for Molecular Dynamics Simulations.mp4
008 Protein Structure Preparation for Molecular Dynamics Simulations_en.srt
009 Preparation of Topology File for Molecular Dynamics Simulations.mp4
009 Preparation of Topology File for Molecular Dynamics Simulations_en.srt
010 Solvation and Ionization of System.mp4
010 Solvation and Ionization of System_en.srt
011 Energy Minimization (EM) of System.mp4
011 Energy Minimization (EM) of System_en.srt
012 Equilibration and Production Phase of Molecular Dynamics Simulation.mp4
012 Equilibration and Production Phase of Molecular Dynamics Simulation_en.srt
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.srt
002 Features of Linux Operating System.mp4
002 Features of Linux Operating System_en.srt
003 Terminal of Linux Operating System.mp4
003 Terminal of Linux Operating System_en.srt
004 Some Basic Commands for Linux Operating System.mp4
004 Some Basic Commands for Linux Operating System_en.srt
005 What's Next.mp4
005 What's Next_en.srt
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.srt
002 Commands-to-Install-GROMACS-Using-Linux-Terminal.pdf
002 Practical-8 Installation of GROMACS.mp4
002 Practical-8 Installation of GROMACS_en.srt
003 Modules of GROMACS Used in Molecular Dynamics Tutorial.mp4
003 Modules of GROMACS Used in Molecular Dynamics Tutorial_en.srt
004 Work Flow of Molecular Dynamics in GROMACS.mp4
004 Work Flow of Molecular Dynamics in GROMACS_en.srt
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations.mp4
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations_en.srt
006 Commands to Run Molecular Dynamics Simulations (For You).mp4
006 Commands to Run Molecular Dynamics Simulations (For You)_en.srt
006 Commands-to-run-MD-simulation-of-Protein-in-Water.pdf
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations.mp4
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations_en.srt
008 Practical-11 Creation of Topology File In GROMACS.mp4
008 Practical-11 Creation of Topology File In GROMACS_en.srt
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation.mp4
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation_en.srt
010 Practical-13 Ionization Step in Molecular Dynamics Simulation.mp4
010 Practical-13 Ionization Step in Molecular Dynamics Simulation_en.srt
010 ions.mdp
011 Practical-14 Energy Minimization (EM) in GROMACS.mp4
011 Practical-14 Energy Minimization (EM) in GROMACS_en.srt
011 minim.mdp
012 Practical-15 Equilibration Phase-I (Part-A).mp4
012 Practical-15 Equilibration Phase-I (Part-A)_en.srt
012 nvt.mdp
013 Practical-16 Equilibration Phase-I (Part-B).mp4
013 Practical-16 Equilibration Phase-I (Part-B)_en.srt
014 Practical-17 Equilibration Phase-II (Part-A).mp4
014 Practical-17 Equilibration Phase-II (Part-A)_en.srt
014 npt.mdp
015 Practical-18 Equilibration Phase-II (Part-B).mp4
015 Practical-18 Equilibration Phase-II (Part-B)_en.srt
016 Understanding md.mdp File Before Final Phase.mp4
016 Understanding md.mdp File Before Final Phase_en.srt
017 Practical-19 Running Molecular Dynamics Simulation Final Phase.mp4
017 Practical-19 Running Molecular Dynamics Simulation Final Phase_en.srt
017 md.mdp
018 Basic Theory of Molecular Dynamics Simulation Data Analysis.mp4
018 Basic Theory of Molecular Dynamics Simulation Data Analysis_en.srt
019 Commands for Analysis of Molecular Dynamics Simulation Data.mp4
019 Commands for Analysis of Molecular Dynamics Simulation Data_en.srt
019 Commands-to-Analyze-the-MD-Data.pdf
020 Bringing the Protein in Center Before Data Analysis.mp4
020 Bringing the Protein in Center Before Data Analysis_en.srt
021 Practical-20 Calculation of RMSD.mp4
021 Practical-20 Calculation of RMSD_en.srt
022 Practical-21 Calculation of RMSF.mp4
022 Practical-21 Calculation of RMSF_en.srt
023 Practical-22 Calculation of Radius of Gyration (Rg).mp4
023 Practical-22 Calculation of Radius of Gyration (Rg)_en.srt
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb).mp4
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)_en.srt
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA).mp4
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)_en.srt
026 Practical-25 Opening of XVG Files in Excel.mp4
026 Practical-25 Opening of XVG Files in Excel_en.srt
027 Practical-25.1 Visualization of MD Trajectory in Pymol.mp4
027 Practical-25.1 Visualization of MD Trajectory in Pymol_en.srt
06 - Module-5 Fundamentals of Molecular Docking (Theory & Practical)
001 Introduction of Docking-Part-1.mp4
001 Introduction of Docking-Part-1_en.srt
002 Introduction of Docking-Part-2.mp4
002 Introduction of Docking-Part-2_en.srt
003 Sampling Algorithms-Part-1.mp4
003 Sampling Algorithms-Part-1_en.srt
004 Sampling Algorithms-Part-2.mp4
004 Sampling Algorithms-Part-2_en.srt
005 Sampling Algorithms-Part-3.mp4
005 Sampling Algorithms-Part-3_en.srt
006 Sampling Algorithms-Part-4.mp4
006 Sampling Algorithms-Part-4_en.srt
007 Scoring Algorithms.mp4
007 Scoring Algorithms_en.srt
008 Types of Docking.mp4
008 Types of Docking_en.srt
009 Basic Steps in Docking Protocol.mp4
009 Basic Steps in Docking Protocol_en.srt
010 Theory of Docking Steps-Part-1.mp4
010 Theory of Docking Steps-Part-1_en.srt
011 Theory of Docking Steps-Part-2.mp4
011 Theory of Docking Steps-Part-2_en.srt
012 MD-3-Installation-of-Docking-Software-10-Silent.txt
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid.mp4
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid_en.srt
013 MD-3-Installation-of-Ligand-Software-11-Silent.txt
013 Practical-27 Installation of Ligand Drawing Tools.mp4
013 Practical-27 Installation of Ligand Drawing Tools_en.srt
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.srt
015 Issue With Protein Structure Preparation in MGL Tools.mp4
015 Issue With Protein Structure Preparation in MGL Tools_en.srt
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database.mp4
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database_en.srt
017 Practical-30 Drawing of Ligand Structure in ChemSketch.mp4
017 Practical-30 Drawing of Ligand Structure in ChemSketch_en.srt
018 Practical-31 Preparation of Ligand Molecule for Docking.mp4
018 Practical-31 Preparation of Ligand Molecule for Docking_en.srt
018 ligand.pdb
019 Practical-32 Prediction of Active Site of Protein.mp4
019 Practical-32 Prediction of Active Site of Protein_en.srt
020 Practical-33 Setting Grid.mp4
020 Practical-33 Setting Grid_en.srt
021 Very Important Step; Be Careful Here.mp4
021 Very Important Step; Be Careful Here_en.srt
022 Practical-34 (Part-A) Performing Docking with Vina.mp4
022 Practical-34 (Part-A) Performing Docking with Vina_en.srt
022 conf.txt
023 Practical-34 (Part-B) Visualization of Vina Docking Data.mp4
023 Practical-34 (Part-B) Visualization of Vina Docking Data_en.srt
024 Practical-35 (Part-A) Performing Docking Using AutoDock4.mp4
024 Practical-35 (Part-A) Performing Docking Using AutoDock4_en.srt
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results.mp4
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results_en.srt
026 Practical-33 Preforming Docking with CB Dock.mp4
026 Practical-33 Preforming Docking with CB Dock_en.srt
027 Practical-34 Analyzing the Docking Data.mp4
027 Practical-34 Analyzing the Docking Data_en.srt
028 Practical-35 PatchDock; Shape Complementary Docking Program.mp4
028 Practical-35 PatchDock; Shape Complementary Docking Program_en.srt
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.srt
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations.mp4
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations_en.srt
003 Basic Steps of Protein-Ligand MD Simulations.mp4
003 Basic Steps of Protein-Ligand MD Simulations_en.srt
004 Practical-36 Very First Step; Preparation of Protein and Ligand.mp4
004 Practical-36 Very First Step; Preparation of Protein and Ligand_en.srt
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations.mp4
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations_en.srt
005 cgenff-charmm2gmx.py
005 em.mdp
005 ie.mdp
005 ions.mdp
005 md.mdp
005 npt.mdp
005 nvt.mdp
005 sort-mol2-bonds.pl
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations.mp4
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations_en.srt
006 Commands-for-MD-Ligand-Protein-Complex.pdf
007 Practical-38 Preparation of Protein Topology File.mp4
007 Practical-38 Preparation of Protein Topology File_en.srt
008 Practical-39 Preparation of Ligand Topology File.mp4
008 Practical-39 Preparation of Ligand Topology File_en.srt
009 Practical-40 Making Complex.mp4
009 Practical-40 Making Complex_en.srt
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex.mp4
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex_en.srt
011 Practical-42 Ligand Restrain.mp4
011 Practical-42 Ligand Restrain_en.srt
012 Practical-43 Thermostats.mp4
012 Practical-43 Thermostats_en.srt
013 Practical-44 Equilibration.mp4
013 Practical-44 Equilibration_en.srt
014 Practical-44 Production Phase.mp4
014 Practical-44 Production Phase_en.srt
015 Commands-to-Analyze-the-Molecular-Dynamics-Simulation-Data-of-Ligand-Protein-Complex.pdf
015 Practical-44 Analysis.mp4
015 Practical-44 Analysis_en.srt
08 - Module-7 Virtual Screening of Drugs
001 Importance of Virtual Screening.mp4
001 Importance of Virtual Screening_en.srt
002 Introduction to Virtual Screening.mp4
002 Introduction to Virtual Screening_en.srt
003 Fundamental Steps of Virtual Screening.mp4
003 Fundamental Steps of Virtual Screening_en.srt
004 Commands Needed to Run Virtual Screening.mp4
004 Commands Needed to Run Virtual Screening_en.srt
004 Commands-to-Run-Vina-for-Virtual-Screening-in-Linux-Environment.pdf
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.srt
006 Practical-47 Preparation of Protein Receptor for Virtual Screening.mp4
006 Practical-47 Preparation of Protein Receptor for Virtual Screening_en.srt
007 Practical-48 Downloading of Thousands of Ligands in One Click.mp4
007 Practical-48 Downloading of Thousands of Ligands in One Click_en.srt
008 Practical-49 Preparation of Ligands for Docking.mp4
008 Practical-49 Preparation of Ligands for Docking_en.srt
009 Practical-50 Setting Grid and Writing of Configuration File.mp4
009 Practical-50 Setting Grid and Writing of Configuration File_en.srt
010 Practical-51 Docking of Ligands with Receptors in Vina.mp4
010 Practical-51 Docking of Ligands with Receptors in Vina_en.srt
010 Vina-linux.pl
011 Practical-52 Analysis.mp4
011 Practical-52 Analysis_en.srt
09 - Recent Updates in Structural Biology For MD and Docking
001 Protein Databank Update.mp4
001 Protein Databank Update_en.srt
Bonus Resources.txt
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