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Udemy Bioinformatics Learn Docking and Mol Dynamics Simulation

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Udemy Bioinformatics Learn Docking and Mol Dynamics Simulation

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Files:

Get Bonus Downloads Here.url 182 bytes
001 Important Massage from Instructors.mp4 4.3 MB
001 Important Massage from Instructors_en.srt 1.0 KB
001 What is Protein.mp4 51.3 MB
001 What is Protein_en.srt 7.8 KB
002 Experimental Techniques to Determine 3D Structure of Protein.mp4 4.6 MB
002 Experimental Techniques to Determine 3D Structure of Protein_en.srt 2.7 KB
003 Practical-1 How To Download Protein Structure From Protein Databank.mp4 90.0 MB
003 Practical-1 How To Download Protein Structure From Protein Databank_en.srt 17.6 KB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol.mp4 35.6 MB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol_en.srt 9.1 KB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded.mp4 16.0 MB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded_en.srt 3.2 KB
006 Practical-3 Fixing Missing Residues Issue With Modeller.mp4 102.1 MB
006 Practical-3 Fixing Missing Residues Issue With Modeller_en.srt 22.1 KB
006 alignment.ali 1.5 KB
006 script1.py 240 bytes
006 script2.py 464 bytes
006 script3.py 553 bytes
007 Intro to Protein 3D Structure Prediction.mp4 2.4 MB
007 Intro to Protein 3D Structure Prediction_en.srt 2.0 KB
008 Modeller-access-in-MAC.mp4 9.4 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology).mp4 259.7 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology)_en.srt 35.4 KB
008 pdb-95.pir 4.8 MB
008 qseq1.ali 1.1 KB
008 script1.py 1.3 KB
008 script2.py 469 bytes
008 script3.py 383 bytes
008 script4.py 410 bytes
008 script5.py 527 bytes
008 tseq1.pdb 640.2 KB
008 tseq2.pdb 640.2 KB
008 tseq3.pdb 640.2 KB
008 tseq4.pdb 640.2 KB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure.mp4 121.9 MB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure_en.srt 15.0 KB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab.mp4 28.9 MB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab_en.srt 7.5 KB
001 Basic Introduction of Molecular Dynamic Simulations and its Steps.mp4 14.9 MB
001 Basic Introduction of Molecular Dynamic Simulations and its Steps_en.srt 1.5 KB
002 Basic Theory of Molecular Dynamics Simulation (Part-1).mp4 5.0 MB
002 Basic Theory of Molecular Dynamics Simulation (Part-1)_en.srt 2.9 KB
003 Basic Theory of Molecular Dynamics Simulation (Part-2).mp4 7.4 MB
003 Basic Theory of Molecular Dynamics Simulation (Part-2)_en.srt 4.3 KB
004 Basic Theory of Molecular Dynamics Simulation (Part-3).mp4 6.4 MB
004 Basic Theory of Molecular Dynamics Simulation (Part-3)_en.srt 3.8 KB
005 Basic Theory of Molecular Dynamics Simulation (Part-4).mp4 6.0 MB
005 Basic Theory of Molecular Dynamics Simulation (Part-4)_en.srt 2.3 KB
006 MD (Molecular Dynamics Simulation) Cycle.mp4 7.9 MB
006 MD (Molecular Dynamics Simulation) Cycle_en.srt 2.7 KB
007 Basic Steps of Molecular Dynamics Simulations.mp4 1.6 MB
007 Basic Steps of Molecular Dynamics Simulations_en.srt 894 bytes
008 Protein Structure Preparation for Molecular Dynamics Simulations.mp4 8.2 MB
008 Protein Structure Preparation for Molecular Dynamics Simulations_en.srt 3.9 KB
009 Preparation of Topology File for Molecular Dynamics Simulations.mp4 5.3 MB
009 Preparation of Topology File for Molecular Dynamics Simulations_en.srt 2.9 KB
010 Solvation and Ionization of System.mp4 20.0 MB
010 Solvation and Ionization of System_en.srt 1.6 KB
011 Energy Minimization (EM) of System.mp4 2.7 MB
011 Energy Minimization (EM) of System_en.srt 1.8 KB
012 Equilibration and Production Phase of Molecular Dynamics Simulation.mp4 16.7 MB
012 Equilibration and Production Phase of Molecular Dynamics Simulation_en.srt 1.9 KB
001 Basic Type of Operating System Available in Market.mp4 4.2 MB
001 Basic Type of Operating System Available in Market_en.srt 2.5 KB
002 Features of Linux Operating System.mp4 4.8 MB
002 Features of Linux Operating System_en.srt 2.8 KB
003 Terminal of Linux Operating System.mp4 1.5 MB
003 Terminal of Linux Operating System_en.srt 1.1 KB
004 Some Basic Commands for Linux Operating System.mp4 26.8 MB
004 Some Basic Commands for Linux Operating System_en.srt 4.6 KB
005 What's Next.mp4 4.2 MB
005 What's Next_en.srt 2.4 KB
001 Practical-7 Installation of Linux in Windows Environment.mp4 30.3 MB
001 Practical-7 Installation of Linux in Windows Environment_en.srt 6.0 KB
002 Commands-to-Install-GROMACS-Using-Linux-Terminal.pdf 91.9 KB
002 Practical-8 Installation of GROMACS.mp4 42.0 MB
002 Practical-8 Installation of GROMACS_en.srt 6.7 KB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial.mp4 4.5 MB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial_en.srt 3.4 KB
004 Work Flow of Molecular Dynamics in GROMACS.mp4 15.1 MB
004 Work Flow of Molecular Dynamics in GROMACS_en.srt 5.6 KB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations.mp4 19.4 MB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations_en.srt 5.0 KB
006 Commands to Run Molecular Dynamics Simulations (For You).mp4 3.6 MB
006 Commands to Run Molecular Dynamics Simulations (For You)_en.srt 1.6 KB
006 Commands-to-run-MD-simulation-of-Protein-in-Water.pdf 87.6 KB
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations.mp4 16.6 MB
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations_en.srt 5.9 KB
008 Practical-11 Creation of Topology File In GROMACS.mp4 49.4 MB
008 Practical-11 Creation of Topology File In GROMACS_en.srt 7.0 KB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation.mp4 41.1 MB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation_en.srt 6.6 KB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation.mp4 34.0 MB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation_en.srt 8.3 KB
010 ions.mdp 1.0 KB
011 Practical-14 Energy Minimization (EM) in GROMACS.mp4 48.5 MB
011 Practical-14 Energy Minimization (EM) in GROMACS_en.srt 6.9 KB
011 minim.mdp 1.0 KB
012 Practical-15 Equilibration Phase-I (Part-A).mp4 21.9 MB
012 Practical-15 Equilibration Phase-I (Part-A)_en.srt 7.6 KB
012 nvt.mdp 2.4 KB
013 Practical-16 Equilibration Phase-I (Part-B).mp4 15.0 MB
013 Practical-16 Equilibration Phase-I (Part-B)_en.srt 3.0 KB
014 Practical-17 Equilibration Phase-II (Part-A).mp4 24.2 MB
014 Practical-17 Equilibration Phase-II (Part-A)_en.srt 3.1 KB
014 npt.mdp 2.6 KB
015 Practical-18 Equilibration Phase-II (Part-B).mp4 14.6 MB
015 Practical-18 Equilibration Phase-II (Part-B)_en.srt 4.3 KB
016 Understanding md.mdp File Before Final Phase.mp4 12.7 MB
016 Understanding md.mdp File Before Final Phase_en.srt 2.8 KB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase.mp4 13.5 MB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase_en.srt 5.2 KB
017 md.mdp 2.7 KB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis.mp4 14.3 MB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis_en.srt 8.1 KB
019 Commands for Analysis of Molecular Dynamics Simulation Data.mp4 7.6 MB
019 Commands for Analysis of Molecular Dynamics Simulation Data_en.srt 1.1 KB
019 Commands-to-Analyze-the-MD-Data.pdf 66.9 KB
020 Bringing the Protein in Center Before Data Analysis.mp4 8.1 MB
020 Bringing the Protein in Center Before Data Analysis_en.srt 4.9 KB
021 Practical-20 Calculation of RMSD.mp4 11.4 MB
021 Practical-20 Calculation of RMSD_en.srt 4.2 KB
022 Practical-21 Calculation of RMSF.mp4 10.8 MB
022 Practical-21 Calculation of RMSF_en.srt 3.5 KB
023 Practical-22 Calculation of Radius of Gyration (Rg).mp4 9.6 MB
023 Practical-22 Calculation of Radius of Gyration (Rg)_en.srt 3.1 KB
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb).mp4 6.8 MB
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)_en.srt 3.7 KB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA).mp4 22.6 MB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)_en.srt 3.3 KB
026 Practical-25 Opening of XVG Files in Excel.mp4 40.6 MB
026 Practical-25 Opening of XVG Files in Excel_en.srt 7.1 KB
027 Practical-25.1 Visualization of MD Trajectory in Pymol.mp4 36.5 MB
027 Practical-25.1 Visualization of MD Trajectory in Pymol_en.srt 5.0 KB
001 Introduction of Docking-Part-1.mp4 3.2 MB
001 Introduction of Docking-Part-1_en.srt 1.7 KB
002 Introduction of Docking-Part-2.mp4 3.0 MB
002 Introduction of Docking-Part-2_en.srt 1.8 KB
003 Sampling Algorithms-Part-1.mp4 1.9 MB
003 Sampling Algorithms-Part-1_en.srt 881 bytes
004 Sampling Algorithms-Part-2.mp4 1.6 MB
004 Sampling Algorithms-Part-2_en.srt 1.3 KB
005 Sampling Algorithms-Part-3.mp4 16.4 MB
005 Sampling Algorithms-Part-3_en.srt 1.5 KB
006 Sampling Algorithms-Part-4.mp4 7.9 MB
006 Sampling Algorithms-Part-4_en.srt 4.0 KB
007 Scoring Algorithms.mp4 5.7 MB
007 Scoring Algorithms_en.srt 3.6 KB
008 Types of Docking.mp4 2.8 MB
008 Types of Docking_en.srt 2.1 KB
009 Basic Steps in Docking Protocol.mp4 8.0 MB
009 Basic Steps in Docking Protocol_en.srt 1.9 KB
010 Theory of Docking Steps-Part-1.mp4 7.0 MB
010 Theory of Docking Steps-Part-1_en.srt 4.2 KB
011 Theory of Docking Steps-Part-2.mp4 5.6 MB
011 Theory of Docking Steps-Part-2_en.srt 3.7 KB
012 MD-3-Installation-of-Docking-Software-10-Silent.txt 366 bytes
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid.mp4 23.0 MB
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid_en.srt 6.4 KB
013 MD-3-Installation-of-Ligand-Software-11-Silent.txt 170 bytes
013 Practical-27 Installation of Ligand Drawing Tools.mp4 12.7 MB
013 Practical-27 Installation of Ligand Drawing Tools_en.srt 5.2 KB
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking.mp4 67.6 MB
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking_en.srt 14.4 KB
015 Issue With Protein Structure Preparation in MGL Tools.mp4 6.9 MB
015 Issue With Protein Structure Preparation in MGL Tools_en.srt 2.4 KB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database.mp4 33.4 MB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database_en.srt 9.5 KB
017 Practical-30 Drawing of Ligand Structure in ChemSketch.mp4 62.2 MB
017 Practical-30 Drawing of Ligand Structure in ChemSketch_en.srt 14.9 KB
018 Practical-31 Preparation of Ligand Molecule for Docking.mp4 54.5 MB
018 Practical-31 Preparation of Ligand Molecule for Docking_en.srt 10.5 KB
018 ligand.pdb 6.6 KB
019 Practical-32 Prediction of Active Site of Protein.mp4 38.2 MB
019 Practical-32 Prediction of Active Site of Protein_en.srt 5.4 KB
020 Practical-33 Setting Grid.mp4 50.1 MB
020 Practical-33 Setting Grid_en.srt 8.8 KB
021 Very Important Step; Be Careful Here.mp4 15.8 MB
021 Very Important Step; Be Careful Here_en.srt 2.7 KB
022 Practical-34 (Part-A) Performing Docking with Vina.mp4 29.7 MB
022 Practical-34 (Part-A) Performing Docking with Vina_en.srt 10.8 KB
022 conf.txt 182 bytes
023 Practical-34 (Part-B) Visualization of Vina Docking Data.mp4 24.6 MB
023 Practical-34 (Part-B) Visualization of Vina Docking Data_en.srt 6.0 KB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4.mp4 83.0 MB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4_en.srt 12.4 KB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results.mp4 21.1 MB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results_en.srt 6.9 KB
026 Practical-33 Preforming Docking with CB Dock.mp4 26.4 MB
026 Practical-33 Preforming Docking with CB Dock_en.srt 9.2 KB
027 Practical-34 Analyzing the Docking Data.mp4 60.9 MB
027 Practical-34 Analyzing the Docking Data_en.srt 13.1 KB
028 Practical-35 PatchDock; Shape Complementary Docking Program.mp4 80.1 MB
028 Practical-35 PatchDock; Shape Complementary Docking Program_en.srt 10.5 KB
001 Biggest Drawback of Conventional Docking Protocol.mp4 5.1 MB
001 Biggest Drawback of Conventional Docking Protocol_en.srt 2.0 KB
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations.mp4 1.4 MB
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations_en.srt 1.2 KB
003 Basic Steps of Protein-Ligand MD Simulations.mp4 3.3 MB
003 Basic Steps of Protein-Ligand MD Simulations_en.srt 1.8 KB
004 Practical-36 Very First Step; Preparation of Protein and Ligand.mp4 29.9 MB
004 Practical-36 Very First Step; Preparation of Protein and Ligand_en.srt 3.9 KB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations.mp4 9.1 MB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations_en.srt 3.3 KB
005 cgenff-charmm2gmx.py 37.0 KB
005 em.mdp 1.1 KB
005 ie.mdp 2.6 KB
005 ions.mdp 1.0 KB
005 md.mdp 2.6 KB
005 npt.mdp 2.7 KB
005 nvt.mdp 2.4 KB
005 sort-mol2-bonds.pl 3.4 KB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations.mp4 3.0 MB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations_en.srt 1.4 KB
006 Commands-for-MD-Ligand-Protein-Complex.pdf 82.0 KB
007 Practical-38 Preparation of Protein Topology File.mp4 31.7 MB
007 Practical-38 Preparation of Protein Topology File_en.srt 5.8 KB
008 Practical-39 Preparation of Ligand Topology File.mp4 35.6 MB
008 Practical-39 Preparation of Ligand Topology File_en.srt 7.9 KB
009 Practical-40 Making Complex.mp4 40.9 MB
009 Practical-40 Making Complex_en.srt 8.6 KB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex.mp4 18.9 MB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex_en.srt 6.1 KB
011 Practical-42 Ligand Restrain.mp4 31.5 MB
011 Practical-42 Ligand Restrain_en.srt 7.5 KB
012 Practical-43 Thermostats.mp4 8.4 MB
012 Practical-43 Thermostats_en.srt 2.9 KB
013 Practical-44 Equilibration.mp4 22.4 MB
013 Practical-44 Equilibration_en.srt 5.5 KB
014 Practical-44 Production Phase.mp4 18.8 MB
014 Practical-44 Production Phase_en.srt 3.3 KB
015 Commands-to-Analyze-the-Molecular-Dynamics-Simulation-Data-of-Ligand-Protein-Complex.pdf 64.4 KB
015 Practical-44 Analysis.mp4 59.7 MB
015 Practical-44 Analysis_en.srt 9.1 KB
001 Importance of Virtual Screening.mp4 23.3 MB
001 Importance of Virtual Screening_en.srt 1.8 KB
002 Introduction to Virtual Screening.mp4 17.0 MB
002 Introduction to Virtual Screening_en.srt 3.7 KB
003 Fundamental Steps of Virtual Screening.mp4 6.5 MB
003 Fundamental Steps of Virtual Screening_en.srt 4.6 KB
004 Commands Needed to Run Virtual Screening.mp4 1.6 MB
004 Commands Needed to Run Virtual Screening_en.srt 923 bytes
004 Commands-to-Run-Vina-for-Virtual-Screening-in-Linux-Environment.pdf 69.4 KB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu).mp4 25.0 MB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)_en.srt 5.5 KB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening.mp4 11.2 MB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening_en.srt 3.4 KB
007 Practical-48 Downloading of Thousands of Ligands in One Click.mp4 43.1 MB
007 Practical-48 Downloading of Thousands of Ligands in One Click_en.srt 7.3 KB
008 Practical-49 Preparation of Ligands for Docking.mp4 24.9 MB
008 Practical-49 Preparation of Ligands for Docking_en.srt 11.7 KB
009 Practical-50 Setting Grid and Writing of Configuration File.mp4 7.2 MB
009 Practical-50 Setting Grid and Writing of Configuration File_en.srt 3.7 KB
010 Practical-51 Docking of Ligands with Receptors in Vina.mp4 27.8 MB
010 Practical-51 Docking of Ligands with Receptors in Vina_en.srt 6.4 KB
010 Vina-linux.pl 409 bytes
011 Practical-52 Analysis.mp4 11.9 MB
011 Practical-52 Analysis_en.srt 2.2 KB
001 Protein Databank Update.mp4 46.1 MB
001 Protein Databank Update_en.srt 6.3 KB
Bonus Resources.txt 386 bytes

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