DevCourseWeb com Udemy Bioinformatics Learn Docking and Mol Dynamics Simulation

DevCourseWeb com Udemy Bioinformatics Learn Docking and Mol Dynamics Simulation

Name	[ DevCourseWeb.com ] Udemy - Bioinformatics; Learn Docking and Mol Dynamics Simulation	DOWNLOAD Copy Link
Total Size	2.9 GB
Total Files	262
Last Seen	2024-11-06 00:33
Hash	AF5D6B0E702BBEFA179120B3FAFEE6C6F68FD7D9

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Get Bonus Downloads Here.url	0.2 KB
/.../01 - Important Massage Before Start of The Course/
001 Important Massage from Instructors.mp4	4.5 MB
001 Important Massage from Instructors_en.srt	1.0 KB
/.../02 - (Optional) Module-1 Protein Structure Basics & Way to Get Them/
001 What is Protein.mp4	53.8 MB
001 What is Protein_en.srt	8.0 KB
002 Experimental Techniques to Determine 3D Structure of Protein.mp4	4.8 MB
002 Experimental Techniques to Determine 3D Structure of Protein_en.srt	2.8 KB
003 Practical-1 How To Download Protein Structure From Protein Databank.mp4	94.4 MB
003 Practical-1 How To Download Protein Structure From Protein Databank_en.srt	18.0 KB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol.mp4	37.3 MB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol_en.srt	9.3 KB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded.mp4	16.8 MB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded_en.srt	3.3 KB
006 Practical-3 Fixing Missing Residues Issue With Modeller.mp4	107.1 MB
006 Practical-3 Fixing Missing Residues Issue With Modeller_en.srt	22.7 KB
006 alignment.ali	1.5 KB
006 script1.py	0.2 KB
006 script2.py	0.5 KB
006 script3.py	0.6 KB
007 Intro to Protein 3D Structure Prediction.mp4	2.5 MB
007 Intro to Protein 3D Structure Prediction_en.srt	2.0 KB
008 Modeller-access-in-MAC.mp4	9.9 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology).mp4	272.3 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology)_en.srt	36.3 KB
008 pdb-95.pir	5.1 MB
008 qseq1.ali	1.1 KB
008 script1.py	1.3 KB
008 script2.py	0.5 KB
008 script3.py	0.4 KB
008 script4.py	0.4 KB
008 script5.py	0.5 KB
008 tseq1.pdb	655.5 KB
008 tseq2.pdb	655.5 KB
008 tseq3.pdb	655.5 KB
008 tseq4.pdb	655.5 KB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure.mp4	127.8 MB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure_en.srt	15.3 KB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab.mp4	30.3 MB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab_en.srt	7.6 KB
/.../03 - Module-2 Theory of Molecular Dynamics Simulations/
001 Basic Introduction of Molecular Dynamic Simulations and its Steps.mp4	15.6 MB
001 Basic Introduction of Molecular Dynamic Simulations and its Steps_en.srt	1.6 KB
002 Basic Theory of Molecular Dynamics Simulation (Part-1).mp4	5.2 MB
002 Basic Theory of Molecular Dynamics Simulation (Part-1)_en.srt	3.0 KB
003 Basic Theory of Molecular Dynamics Simulation (Part-2).mp4	7.8 MB
003 Basic Theory of Molecular Dynamics Simulation (Part-2)_en.srt	4.4 KB
004 Basic Theory of Molecular Dynamics Simulation (Part-3).mp4	6.7 MB
004 Basic Theory of Molecular Dynamics Simulation (Part-3)_en.srt	3.9 KB
005 Basic Theory of Molecular Dynamics Simulation (Part-4).mp4	6.3 MB
005 Basic Theory of Molecular Dynamics Simulation (Part-4)_en.srt	2.3 KB
006 MD (Molecular Dynamics Simulation) Cycle.mp4	8.3 MB
006 MD (Molecular Dynamics Simulation) Cycle_en.srt	2.8 KB
007 Basic Steps of Molecular Dynamics Simulations.mp4	1.7 MB
007 Basic Steps of Molecular Dynamics Simulations_en.srt	0.9 KB
008 Protein Structure Preparation for Molecular Dynamics Simulations.mp4	8.6 MB
008 Protein Structure Preparation for Molecular Dynamics Simulations_en.srt	4.0 KB
009 Preparation of Topology File for Molecular Dynamics Simulations.mp4	5.5 MB
009 Preparation of Topology File for Molecular Dynamics Simulations_en.srt	2.9 KB
010 Solvation and Ionization of System.mp4	21.0 MB
010 Solvation and Ionization of System_en.srt	1.6 KB
011 Energy Minimization (EM) of System.mp4	2.9 MB
011 Energy Minimization (EM) of System_en.srt	1.8 KB
012 Equilibration and Production Phase of Molecular Dynamics Simulation.mp4	17.6 MB
012 Equilibration and Production Phase of Molecular Dynamics Simulation_en.srt	2.0 KB
/.../04 - Module 3 Computer Operating System Used for Molecular Dynamics Simulation/
001 Basic Type of Operating System Available in Market.mp4	4.4 MB
001 Basic Type of Operating System Available in Market_en.srt	2.6 KB
002 Features of Linux Operating System.mp4	5.0 MB
002 Features of Linux Operating System_en.srt	2.9 KB
003 Terminal of Linux Operating System.mp4	1.6 MB
003 Terminal of Linux Operating System_en.srt	1.2 KB
004 Some Basic Commands for Linux Operating System.mp4	28.1 MB
004 Some Basic Commands for Linux Operating System_en.srt	4.7 KB
005 What's Next.mp4	4.4 MB
005 What's Next_en.srt	2.4 KB
/.../05 - Module 4 Demonstration of MD Simulation of Protein in Water with GROMACS/
001 Practical-7 Installation of Linux in Windows Environment.mp4	31.8 MB
001 Practical-7 Installation of Linux in Windows Environment_en.srt	6.1 KB
002 Commands-to-Install-GROMACS-Using-Linux-Terminal.pdf	94.1 KB
002 Practical-8 Installation of GROMACS.mp4	44.1 MB
002 Practical-8 Installation of GROMACS_en.srt	6.9 KB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial.mp4	4.7 MB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial_en.srt	3.5 KB
004 Work Flow of Molecular Dynamics in GROMACS.mp4	15.8 MB
004 Work Flow of Molecular Dynamics in GROMACS_en.srt	5.8 KB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations.mp4	20.3 MB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations_en.srt	5.1 KB
006 Commands to Run Molecular Dynamics Simulations (For You).mp4	3.8 MB
006 Commands to Run Molecular Dynamics Simulations (For You)_en.srt	1.7 KB
006 Commands-to-run-MD-simulation-of-Protein-in-Water.pdf	89.7 KB
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations.mp4	17.4 MB
007 Practical-10 Cleaning Protein Structure For Molecular Dynamics Simulations_en.srt	6.1 KB
008 Practical-11 Creation of Topology File In GROMACS.mp4	51.8 MB
008 Practical-11 Creation of Topology File In GROMACS_en.srt	7.2 KB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation.mp4	43.1 MB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation_en.srt	6.7 KB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation.mp4	35.6 MB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation_en.srt	8.5 KB
010 ions.mdp	1.1 KB
011 Practical-14 Energy Minimization (EM) in GROMACS.mp4	50.9 MB
011 Practical-14 Energy Minimization (EM) in GROMACS_en.srt	7.1 KB
011 minim.mdp	1.1 KB
012 Practical-15 Equilibration Phase-I (Part-A).mp4	23.0 MB
012 Practical-15 Equilibration Phase-I (Part-A)_en.srt	7.8 KB
012 nvt.mdp	2.4 KB
013 Practical-16 Equilibration Phase-I (Part-B).mp4	15.7 MB
013 Practical-16 Equilibration Phase-I (Part-B)_en.srt	3.1 KB
014 Practical-17 Equilibration Phase-II (Part-A).mp4	25.4 MB
014 Practical-17 Equilibration Phase-II (Part-A)_en.srt	3.2 KB
014 npt.mdp	2.6 KB
015 Practical-18 Equilibration Phase-II (Part-B).mp4	15.3 MB
015 Practical-18 Equilibration Phase-II (Part-B)_en.srt	4.4 KB
016 Understanding md.mdp File Before Final Phase.mp4	13.3 MB
016 Understanding md.mdp File Before Final Phase_en.srt	2.9 KB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase.mp4	14.1 MB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase_en.srt	5.3 KB
017 md.mdp	2.8 KB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis.mp4	15.0 MB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis_en.srt	8.3 KB
019 Commands for Analysis of Molecular Dynamics Simulation Data.mp4	7.9 MB
019 Commands for Analysis of Molecular Dynamics Simulation Data_en.srt	1.2 KB
019 Commands-to-Analyze-the-MD-Data.pdf	68.5 KB
020 Bringing the Protein in Center Before Data Analysis.mp4	8.5 MB
020 Bringing the Protein in Center Before Data Analysis_en.srt	5.0 KB
021 Practical-20 Calculation of RMSD.mp4	12.0 MB
021 Practical-20 Calculation of RMSD_en.srt	4.3 KB
022 Practical-21 Calculation of RMSF.mp4	11.4 MB
022 Practical-21 Calculation of RMSF_en.srt	3.6 KB
023 Practical-22 Calculation of Radius of Gyration (Rg).mp4	10.1 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	7.1 MB
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)_en.srt	3.8 KB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA).mp4	23.7 MB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)_en.srt	3.4 KB
026 Practical-25 Opening of XVG Files in Excel.mp4	42.6 MB
026 Practical-25 Opening of XVG Files in Excel_en.srt	7.2 KB
027 Practical-25.1 Visualization of MD Trajectory in Pymol.mp4	38.3 MB
027 Practical-25.1 Visualization of MD Trajectory in Pymol_en.srt	5.2 KB
/.../06 - Module-5 Fundamentals of Molecular Docking (Theory & Practical)/
001 Introduction of Docking-Part-1.mp4	3.3 MB
001 Introduction of Docking-Part-1_en.srt	1.8 KB
002 Introduction of Docking-Part-2.mp4	3.1 MB
002 Introduction of Docking-Part-2_en.srt	1.8 KB
003 Sampling Algorithms-Part-1.mp4	2.0 MB
003 Sampling Algorithms-Part-1_en.srt	0.9 KB
004 Sampling Algorithms-Part-2.mp4	1.7 MB
004 Sampling Algorithms-Part-2_en.srt	1.3 KB
005 Sampling Algorithms-Part-3.mp4	17.2 MB
005 Sampling Algorithms-Part-3_en.srt	1.5 KB
006 Sampling Algorithms-Part-4.mp4	8.3 MB
006 Sampling Algorithms-Part-4_en.srt	4.1 KB
007 Scoring Algorithms.mp4	6.0 MB
007 Scoring Algorithms_en.srt	3.7 KB
008 Types of Docking.mp4	2.9 MB
008 Types of Docking_en.srt	2.1 KB
009 Basic Steps in Docking Protocol.mp4	8.4 MB
009 Basic Steps in Docking Protocol_en.srt	2.0 KB
010 Theory of Docking Steps-Part-1.mp4	7.4 MB
010 Theory of Docking Steps-Part-1_en.srt	4.3 KB
011 Theory of Docking Steps-Part-2.mp4	5.9 MB
011 Theory of Docking Steps-Part-2_en.srt	3.8 KB
012 MD-3-Installation-of-Docking-Software-10-Silent.txt	0.4 KB
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid.mp4	24.1 MB
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid_en.srt	6.6 KB
013 MD-3-Installation-of-Ligand-Software-11-Silent.txt	0.2 KB
013 Practical-27 Installation of Ligand Drawing Tools.mp4	13.3 MB
013 Practical-27 Installation of Ligand Drawing Tools_en.srt	5.3 KB
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking.mp4	70.8 MB
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking_en.srt	14.8 KB
015 Issue With Protein Structure Preparation in MGL Tools.mp4	7.3 MB
015 Issue With Protein Structure Preparation in MGL Tools_en.srt	2.5 KB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database.mp4	35.1 MB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database_en.srt	9.7 KB
017 Practical-30 Drawing of Ligand Structure in ChemSketch.mp4	65.2 MB
017 Practical-30 Drawing of Ligand Structure in ChemSketch_en.srt	15.2 KB
018 Practical-31 Preparation of Ligand Molecule for Docking.mp4	57.2 MB
018 Practical-31 Preparation of Ligand Molecule for Docking_en.srt	10.7 KB
018 ligand.pdb	6.7 KB
019 Practical-32 Prediction of Active Site of Protein.mp4	40.0 MB
019 Practical-32 Prediction of Active Site of Protein_en.srt	5.6 KB
020 Practical-33 Setting Grid.mp4	52.5 MB
020 Practical-33 Setting Grid_en.srt	9.0 KB
021 Very Important Step; Be Careful Here.mp4	16.6 MB
021 Very Important Step; Be Careful Here_en.srt	2.8 KB
022 Practical-34 (Part-A) Performing Docking with Vina.mp4	31.1 MB
022 Practical-34 (Part-A) Performing Docking with Vina_en.srt	11.1 KB
022 conf.txt	0.2 KB
023 Practical-34 (Part-B) Visualization of Vina Docking Data.mp4	25.8 MB
023 Practical-34 (Part-B) Visualization of Vina Docking Data_en.srt	6.1 KB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4.mp4	87.0 MB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4_en.srt	12.7 KB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results.mp4	22.1 MB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results_en.srt	7.1 KB
026 Practical-33 Preforming Docking with CB Dock.mp4	27.7 MB
026 Practical-33 Preforming Docking with CB Dock_en.srt	9.4 KB
027 Practical-34 Analyzing the Docking Data.mp4	63.9 MB
027 Practical-34 Analyzing the Docking Data_en.srt	13.4 KB
028 Practical-35 PatchDock; Shape Complementary Docking Program.mp4	83.9 MB
028 Practical-35 PatchDock; Shape Complementary Docking Program_en.srt	10.8 KB
/.../07 - Module-6 Molecular Dynamics Simulations of Protein-Ligand Docked Complex/
001 Biggest Drawback of Conventional Docking Protocol.mp4	5.3 MB
001 Biggest Drawback of Conventional Docking Protocol_en.srt	2.1 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	1.3 KB
003 Basic Steps of Protein-Ligand MD Simulations.mp4	3.5 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	31.4 MB
004 Practical-36 Very First Step; Preparation of Protein and Ligand_en.srt	4.0 KB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations.mp4	9.6 MB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations_en.srt	3.4 KB
005 cgenff-charmm2gmx.py	37.8 KB
005 em.mdp	1.2 KB
005 ie.mdp	2.7 KB
005 ions.mdp	1.0 KB
005 md.mdp	2.6 KB
005 npt.mdp	2.7 KB
005 nvt.mdp	2.5 KB
005 sort-mol2-bonds.pl	3.5 KB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations.mp4	3.1 MB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations_en.srt	1.4 KB
006 Commands-for-MD-Ligand-Protein-Complex.pdf	84.0 KB
007 Practical-38 Preparation of Protein Topology File.mp4	33.2 MB
007 Practical-38 Preparation of Protein Topology File_en.srt	5.9 KB
008 Practical-39 Preparation of Ligand Topology File.mp4	37.3 MB
008 Practical-39 Preparation of Ligand Topology File_en.srt	8.1 KB
009 Practical-40 Making Complex.mp4	42.9 MB
009 Practical-40 Making Complex_en.srt	8.8 KB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex.mp4	19.8 MB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex_en.srt	6.3 KB
011 Practical-42 Ligand Restrain.mp4	33.0 MB
011 Practical-42 Ligand Restrain_en.srt	7.7 KB
012 Practical-43 Thermostats.mp4	8.8 MB
012 Practical-43 Thermostats_en.srt	2.9 KB
013 Practical-44 Equilibration.mp4	23.5 MB
013 Practical-44 Equilibration_en.srt	5.6 KB
014 Practical-44 Production Phase.mp4	19.7 MB
014 Practical-44 Production Phase_en.srt	3.4 KB
015 Commands-to-Analyze-the-Molecular-Dynamics-Simulation-Data-of-Ligand-Protein-Complex.pdf	65.9 KB
015 Practical-44 Analysis.mp4	62.6 MB
015 Practical-44 Analysis_en.srt	9.4 KB
/.../08 - Module-7 Virtual Screening of Drugs/
001 Importance of Virtual Screening.mp4	24.4 MB
001 Importance of Virtual Screening_en.srt	1.9 KB
002 Introduction to Virtual Screening.mp4	17.8 MB
002 Introduction to Virtual Screening_en.srt	3.8 KB
003 Fundamental Steps of Virtual Screening.mp4	6.8 MB
003 Fundamental Steps of Virtual Screening_en.srt	4.7 KB
004 Commands Needed to Run Virtual Screening.mp4	1.7 MB
004 Commands Needed to Run Virtual Screening_en.srt	0.9 KB
004 Commands-to-Run-Vina-for-Virtual-Screening-in-Linux-Environment.pdf	71.1 KB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu).mp4	26.2 MB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)_en.srt	5.7 KB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening.mp4	11.8 MB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening_en.srt	3.5 KB
007 Practical-48 Downloading of Thousands of Ligands in One Click.mp4	45.2 MB
007 Practical-48 Downloading of Thousands of Ligands in One Click_en.srt	7.5 KB
008 Practical-49 Preparation of Ligands for Docking.mp4	26.1 MB
008 Practical-49 Preparation of Ligands for Docking_en.srt	12.0 KB
009 Practical-50 Setting Grid and Writing of Configuration File.mp4	7.6 MB
009 Practical-50 Setting Grid and Writing of Configuration File_en.srt	3.8 KB
010 Practical-51 Docking of Ligands with Receptors in Vina.mp4	29.2 MB
010 Practical-51 Docking of Ligands with Receptors in Vina_en.srt	6.6 KB
010 Vina-linux.pl	0.4 KB
011 Practical-52 Analysis.mp4	12.5 MB
011 Practical-52 Analysis_en.srt	2.2 KB
/.../09 - Recent Updates in Structural Biology For MD and Docking/
001 Protein Databank Update.mp4	48.4 MB
001 Protein Databank Update_en.srt	6.5 KB
/~Get Your Files Here !/
Bonus Resources.txt	0.4 KB
Total files 262