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[ DevCourseWeb.com ] Udemy - Bioinformatics; Learn Docking and Mol Dynamics Simulation
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[ DevCourseWeb.com ] Udemy - Bioinformatics; Learn Docking and Mol Dynamics Simulation
Get Bonus Downloads Here.url
- 182 B
~Get Your Files Here !
01 - Important Massage Before Start of The Course
001 Important Massage from Instructors.mp4
- 4.26 MB
001 Important Massage from Instructors_en.srt
- 1.02 KB
02 - (Optional) Module-1 Protein Structure Basics & Way to Get Them
001 What is Protein.mp4
- 51.3 MB
001 What is Protein_en.srt
- 7.85 KB
002 Experimental Techniques to Determine 3D Structure of Protein.mp4
- 4.59 MB
002 Experimental Techniques to Determine 3D Structure of Protein_en.srt
- 2.75 KB
003 Practical-1 How To Download Protein Structure From Protein Databank.mp4
- 90 MB
003 Practical-1 How To Download Protein Structure From Protein Databank_en.srt
- 17.62 KB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol.mp4
- 35.58 MB
004 Practical-2 Visualization of 3D Structure of Protein Using Pymol_en.srt
- 9.08 KB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded.mp4
- 16.03 MB
005 Fixing the Missing Residues in Protein 3D Structure Downloaded_en.srt
- 3.24 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
- 22.12 KB
006 alignment.ali
- 1.45 KB
006 script1.py
- 240 B
006 script2.py
- 464 B
006 script3.py
- 553 B
007 Intro to Protein 3D Structure Prediction.mp4
- 2.41 MB
007 Intro to Protein 3D Structure Prediction_en.srt
- 1.99 KB
008 Modeller-access-in-MAC.mp4
- 9.45 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology).mp4
- 259.72 MB
008 Practical-4 How to Predict 3D Structure Using Modeller (Homology)_en.srt
- 35.44 KB
008 pdb-95.pir
- 4.83 MB
008 qseq1.ali
- 1.1 KB
008 script1.py
- 1.3 KB
008 script2.py
- 469 B
008 script3.py
- 383 B
008 script4.py
- 410 B
008 script5.py
- 527 B
008 tseq1.pdb
- 640.18 KB
008 tseq2.pdb
- 640.18 KB
008 tseq3.pdb
- 640.18 KB
008 tseq4.pdb
- 640.18 KB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure.mp4
- 121.93 MB
009 Practical-5 How to Use I-TASSER for Prediction of 3D Structure_en.srt
- 14.99 KB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab.mp4
- 28.86 MB
010 Practical-6 Introduction of Alpha-Fold Database and Alpha-Fold Colab_en.srt
- 7.45 KB
03 - Module-2 Theory of Molecular Dynamics Simulations
001 Basic Introduction of Molecular Dynamic Simulations and its Steps.mp4
- 14.92 MB
001 Basic Introduction of Molecular Dynamic Simulations and its Steps_en.srt
- 1.55 KB
002 Basic Theory of Molecular Dynamics Simulation (Part-1).mp4
- 4.97 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
- 7.43 MB
003 Basic Theory of Molecular Dynamics Simulation (Part-2)_en.srt
- 4.33 KB
004 Basic Theory of Molecular Dynamics Simulation (Part-3).mp4
- 6.42 MB
004 Basic Theory of Molecular Dynamics Simulation (Part-3)_en.srt
- 3.81 KB
005 Basic Theory of Molecular Dynamics Simulation (Part-4).mp4
- 5.99 MB
005 Basic Theory of Molecular Dynamics Simulation (Part-4)_en.srt
- 2.28 KB
006 MD (Molecular Dynamics Simulation) Cycle.mp4
- 7.9 MB
006 MD (Molecular Dynamics Simulation) Cycle_en.srt
- 2.75 KB
007 Basic Steps of Molecular Dynamics Simulations.mp4
- 1.62 MB
007 Basic Steps of Molecular Dynamics Simulations_en.srt
- 894 B
008 Protein Structure Preparation for Molecular Dynamics Simulations.mp4
- 8.18 MB
008 Protein Structure Preparation for Molecular Dynamics Simulations_en.srt
- 3.91 KB
009 Preparation of Topology File for Molecular Dynamics Simulations.mp4
- 5.29 MB
009 Preparation of Topology File for Molecular Dynamics Simulations_en.srt
- 2.86 KB
010 Solvation and Ionization of System.mp4
- 20.04 MB
010 Solvation and Ionization of System_en.srt
- 1.58 KB
011 Energy Minimization (EM) of System.mp4
- 2.74 MB
011 Energy Minimization (EM) of System_en.srt
- 1.75 KB
012 Equilibration and Production Phase of Molecular Dynamics Simulation.mp4
- 16.74 MB
012 Equilibration and Production Phase of Molecular Dynamics Simulation_en.srt
- 1.93 KB
04 - Module 3 Computer Operating System Used for Molecular Dynamics Simulation
001 Basic Type of Operating System Available in Market.mp4
- 4.17 MB
001 Basic Type of Operating System Available in Market_en.srt
- 2.52 KB
002 Features of Linux Operating System.mp4
- 4.77 MB
002 Features of Linux Operating System_en.srt
- 2.83 KB
003 Terminal of Linux Operating System.mp4
- 1.5 MB
003 Terminal of Linux Operating System_en.srt
- 1.15 KB
004 Some Basic Commands for Linux Operating System.mp4
- 26.76 MB
004 Some Basic Commands for Linux Operating System_en.srt
- 4.55 KB
005 What's Next.mp4
- 4.23 MB
005 What's Next_en.srt
- 2.38 KB
05 - Module 4 Demonstration of MD Simulation of Protein in Water with GROMACS
001 Practical-7 Installation of Linux in Windows Environment.mp4
- 30.3 MB
001 Practical-7 Installation of Linux in Windows Environment_en.srt
- 5.96 KB
002 Commands-to-Install-GROMACS-Using-Linux-Terminal.pdf
- 91.94 KB
002 Practical-8 Installation of GROMACS.mp4
- 42.05 MB
002 Practical-8 Installation of GROMACS_en.srt
- 6.72 KB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial.mp4
- 4.48 MB
003 Modules of GROMACS Used in Molecular Dynamics Tutorial_en.srt
- 3.41 KB
004 Work Flow of Molecular Dynamics in GROMACS.mp4
- 15.05 MB
004 Work Flow of Molecular Dynamics in GROMACS_en.srt
- 5.64 KB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations.mp4
- 19.35 MB
005 Practical-9 Creating Folder in Ubuntu For Molecular Dynamics Simulations_en.srt
- 4.99 KB
006 Commands to Run Molecular Dynamics Simulations (For You).mp4
- 3.61 MB
006 Commands to Run Molecular Dynamics Simulations (For You)_en.srt
- 1.63 KB
006 Commands-to-run-MD-simulation-of-Protein-in-Water.pdf
- 87.63 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
- 5.93 KB
008 Practical-11 Creation of Topology File In GROMACS.mp4
- 49.44 MB
008 Practical-11 Creation of Topology File In GROMACS_en.srt
- 7.04 KB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation.mp4
- 41.12 MB
009 Practical-12 Solvation of Step in Molecular Dynamics Simulation_en.srt
- 6.57 KB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation.mp4
- 34 MB
010 Practical-13 Ionization Step in Molecular Dynamics Simulation_en.srt
- 8.33 KB
010 ions.mdp
- 1.03 KB
011 Practical-14 Energy Minimization (EM) in GROMACS.mp4
- 48.54 MB
011 Practical-14 Energy Minimization (EM) in GROMACS_en.srt
- 6.93 KB
011 minim.mdp
- 1.03 KB
012 Practical-15 Equilibration Phase-I (Part-A).mp4
- 21.92 MB
012 Practical-15 Equilibration Phase-I (Part-A)_en.srt
- 7.63 KB
012 nvt.mdp
- 2.35 KB
013 Practical-16 Equilibration Phase-I (Part-B).mp4
- 14.98 MB
013 Practical-16 Equilibration Phase-I (Part-B)_en.srt
- 3.05 KB
014 Practical-17 Equilibration Phase-II (Part-A).mp4
- 24.25 MB
014 Practical-17 Equilibration Phase-II (Part-A)_en.srt
- 3.13 KB
014 npt.mdp
- 2.57 KB
015 Practical-18 Equilibration Phase-II (Part-B).mp4
- 14.56 MB
015 Practical-18 Equilibration Phase-II (Part-B)_en.srt
- 4.31 KB
016 Understanding md.mdp File Before Final Phase.mp4
- 12.72 MB
016 Understanding md.mdp File Before Final Phase_en.srt
- 2.79 KB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase.mp4
- 13.46 MB
017 Practical-19 Running Molecular Dynamics Simulation Final Phase_en.srt
- 5.22 KB
017 md.mdp
- 2.72 KB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis.mp4
- 14.28 MB
018 Basic Theory of Molecular Dynamics Simulation Data Analysis_en.srt
- 8.15 KB
019 Commands for Analysis of Molecular Dynamics Simulation Data.mp4
- 7.55 MB
019 Commands for Analysis of Molecular Dynamics Simulation Data_en.srt
- 1.14 KB
019 Commands-to-Analyze-the-MD-Data.pdf
- 66.85 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
- 4.85 KB
021 Practical-20 Calculation of RMSD.mp4
- 11.45 MB
021 Practical-20 Calculation of RMSD_en.srt
- 4.16 KB
022 Practical-21 Calculation of RMSF.mp4
- 10.84 MB
022 Practical-21 Calculation of RMSF_en.srt
- 3.55 KB
023 Practical-22 Calculation of Radius of Gyration (Rg).mp4
- 9.63 MB
023 Practical-22 Calculation of Radius of Gyration (Rg)_en.srt
- 3.07 KB
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb).mp4
- 6.78 MB
024 Practical-23 Calculation of Total Number of Hydrogen bonds (Hb)_en.srt
- 3.69 KB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA).mp4
- 22.56 MB
025 Practical-24 Calculation of Solvent Accessible Surface Area (SASA)_en.srt
- 3.33 KB
026 Practical-25 Opening of XVG Files in Excel.mp4
- 40.65 MB
026 Practical-25 Opening of XVG Files in Excel_en.srt
- 7.06 KB
027 Practical-25.1 Visualization of MD Trajectory in Pymol.mp4
- 36.54 MB
027 Practical-25.1 Visualization of MD Trajectory in Pymol_en.srt
- 5.05 KB
06 - Module-5 Fundamentals of Molecular Docking (Theory & Practical)
001 Introduction of Docking-Part-1.mp4
- 3.19 MB
001 Introduction of Docking-Part-1_en.srt
- 1.73 KB
002 Introduction of Docking-Part-2.mp4
- 3 MB
002 Introduction of Docking-Part-2_en.srt
- 1.76 KB
003 Sampling Algorithms-Part-1.mp4
- 1.91 MB
003 Sampling Algorithms-Part-1_en.srt
- 881 B
004 Sampling Algorithms-Part-2.mp4
- 1.65 MB
004 Sampling Algorithms-Part-2_en.srt
- 1.28 KB
005 Sampling Algorithms-Part-3.mp4
- 16.36 MB
005 Sampling Algorithms-Part-3_en.srt
- 1.49 KB
006 Sampling Algorithms-Part-4.mp4
- 7.88 MB
006 Sampling Algorithms-Part-4_en.srt
- 3.99 KB
007 Scoring Algorithms.mp4
- 5.68 MB
007 Scoring Algorithms_en.srt
- 3.64 KB
008 Types of Docking.mp4
- 2.81 MB
008 Types of Docking_en.srt
- 2.08 KB
009 Basic Steps in Docking Protocol.mp4
- 7.99 MB
009 Basic Steps in Docking Protocol_en.srt
- 1.9 KB
010 Theory of Docking Steps-Part-1.mp4
- 7.04 MB
010 Theory of Docking Steps-Part-1_en.srt
- 4.25 KB
011 Theory of Docking Steps-Part-2.mp4
- 5.62 MB
011 Theory of Docking Steps-Part-2_en.srt
- 3.72 KB
012 MD-3-Installation-of-Docking-Software-10-Silent.txt
- 366 B
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid.mp4
- 22.95 MB
012 Practical-26 Installation of MGL Tools, Vina, AutoDock4 & Autogrid_en.srt
- 6.41 KB
013 MD-3-Installation-of-Ligand-Software-11-Silent.txt
- 170 B
013 Practical-27 Installation of Ligand Drawing Tools.mp4
- 12.66 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
- 67.57 MB
014 Practical-28 Downloading and Preparation of Protein 3D Structure for Docking_en.srt
- 14.41 KB
015 Issue With Protein Structure Preparation in MGL Tools.mp4
- 6.93 MB
015 Issue With Protein Structure Preparation in MGL Tools_en.srt
- 2.44 KB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database.mp4
- 33.43 MB
016 Practical-29 Downloading of Ligand 3D Structure from ZINC Database_en.srt
- 9.51 KB
017 Practical-30 Drawing of Ligand Structure in ChemSketch.mp4
- 62.18 MB
017 Practical-30 Drawing of Ligand Structure in ChemSketch_en.srt
- 14.88 KB
018 Practical-31 Preparation of Ligand Molecule for Docking.mp4
- 54.51 MB
018 Practical-31 Preparation of Ligand Molecule for Docking_en.srt
- 10.45 KB
018 ligand.pdb
- 6.56 KB
019 Practical-32 Prediction of Active Site of Protein.mp4
- 38.15 MB
019 Practical-32 Prediction of Active Site of Protein_en.srt
- 5.44 KB
020 Practical-33 Setting Grid.mp4
- 50.07 MB
020 Practical-33 Setting Grid_en.srt
- 8.79 KB
021 Very Important Step; Be Careful Here.mp4
- 15.78 MB
021 Very Important Step; Be Careful Here_en.srt
- 2.75 KB
022 Practical-34 (Part-A) Performing Docking with Vina.mp4
- 29.67 MB
022 Practical-34 (Part-A) Performing Docking with Vina_en.srt
- 10.85 KB
022 conf.txt
- 182 B
023 Practical-34 (Part-B) Visualization of Vina Docking Data.mp4
- 24.59 MB
023 Practical-34 (Part-B) Visualization of Vina Docking Data_en.srt
- 5.97 KB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4.mp4
- 83.01 MB
024 Practical-35 (Part-A) Performing Docking Using AutoDock4_en.srt
- 12.42 KB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results.mp4
- 21.08 MB
025 Practical-35 (Part-B) Visualization of AutoDock4 Docking Results_en.srt
- 6.93 KB
026 Practical-33 Preforming Docking with CB Dock.mp4
- 26.43 MB
026 Practical-33 Preforming Docking with CB Dock_en.srt
- 9.21 KB
027 Practical-34 Analyzing the Docking Data.mp4
- 60.91 MB
027 Practical-34 Analyzing the Docking Data_en.srt
- 13.12 KB
028 Practical-35 PatchDock; Shape Complementary Docking Program.mp4
- 80.05 MB
028 Practical-35 PatchDock; Shape Complementary Docking Program_en.srt
- 10.51 KB
07 - Module-6 Molecular Dynamics Simulations of Protein-Ligand Docked Complex
001 Biggest Drawback of Conventional Docking Protocol.mp4
- 5.06 MB
001 Biggest Drawback of Conventional Docking Protocol_en.srt
- 2.02 KB
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations.mp4
- 1.37 MB
002 Difference Between Simple MD Simulation Vs Protein-Ligand MD Simulations_en.srt
- 1.23 KB
003 Basic Steps of Protein-Ligand MD Simulations.mp4
- 3.31 MB
003 Basic Steps of Protein-Ligand MD Simulations_en.srt
- 1.79 KB
004 Practical-36 Very First Step; Preparation of Protein and Ligand.mp4
- 29.94 MB
004 Practical-36 Very First Step; Preparation of Protein and Ligand_en.srt
- 3.86 KB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations.mp4
- 9.15 MB
005 Practical-37 Necessary Files Needed For Molecular Dynamics Simulations_en.srt
- 3.29 KB
005 cgenff-charmm2gmx.py
- 36.95 KB
005 em.mdp
- 1.14 KB
005 ie.mdp
- 2.61 KB
005 ions.mdp
- 1.01 KB
005 md.mdp
- 2.57 KB
005 npt.mdp
- 2.67 KB
005 nvt.mdp
- 2.44 KB
005 sort-mol2-bonds.pl
- 3.41 KB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations.mp4
- 2.97 MB
006 Commands to Run Ligand-Protein Molecular Dynamics Simulations_en.srt
- 1.36 KB
006 Commands-for-MD-Ligand-Protein-Complex.pdf
- 81.98 KB
007 Practical-38 Preparation of Protein Topology File.mp4
- 31.66 MB
007 Practical-38 Preparation of Protein Topology File_en.srt
- 5.78 KB
008 Practical-39 Preparation of Ligand Topology File.mp4
- 35.56 MB
008 Practical-39 Preparation of Ligand Topology File_en.srt
- 7.94 KB
009 Practical-40 Making Complex.mp4
- 40.89 MB
009 Practical-40 Making Complex_en.srt
- 8.56 KB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex.mp4
- 18.93 MB
010 Practical-41 Solvation, Ionization & Energy Minimization of Complex_en.srt
- 6.13 KB
011 Practical-42 Ligand Restrain.mp4
- 31.45 MB
011 Practical-42 Ligand Restrain_en.srt
- 7.48 KB
012 Practical-43 Thermostats.mp4
- 8.44 MB
012 Practical-43 Thermostats_en.srt
- 2.86 KB
013 Practical-44 Equilibration.mp4
- 22.38 MB
013 Practical-44 Equilibration_en.srt
- 5.48 KB
014 Practical-44 Production Phase.mp4
- 18.79 MB
014 Practical-44 Production Phase_en.srt
- 3.32 KB
015 Commands-to-Analyze-the-Molecular-Dynamics-Simulation-Data-of-Ligand-Protein-Complex.pdf
- 64.36 KB
015 Practical-44 Analysis.mp4
- 59.73 MB
015 Practical-44 Analysis_en.srt
- 9.14 KB
08 - Module-7 Virtual Screening of Drugs
001 Importance of Virtual Screening.mp4
- 23.26 MB
001 Importance of Virtual Screening_en.srt
- 1.82 KB
002 Introduction to Virtual Screening.mp4
- 16.96 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
- 4.57 KB
004 Commands Needed to Run Virtual Screening.mp4
- 1.59 MB
004 Commands Needed to Run Virtual Screening_en.srt
- 923 B
004 Commands-to-Run-Vina-for-Virtual-Screening-in-Linux-Environment.pdf
- 69.45 KB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu).mp4
- 24.99 MB
005 Practical-46 Installation of Open Babel and Auto-Dock Vina In Linux (Ubuntu)_en.srt
- 5.54 KB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening.mp4
- 11.24 MB
006 Practical-47 Preparation of Protein Receptor for Virtual Screening_en.srt
- 3.45 KB
007 Practical-48 Downloading of Thousands of Ligands in One Click.mp4
- 43.14 MB
007 Practical-48 Downloading of Thousands of Ligands in One Click_en.srt
- 7.31 KB
008 Practical-49 Preparation of Ligands for Docking.mp4
- 24.93 MB
008 Practical-49 Preparation of Ligands for Docking_en.srt
- 11.73 KB
009 Practical-50 Setting Grid and Writing of Configuration File.mp4
- 7.22 MB
009 Practical-50 Setting Grid and Writing of Configuration File_en.srt
- 3.71 KB
010 Practical-51 Docking of Ligands with Receptors in Vina.mp4
- 27.83 MB
010 Practical-51 Docking of Ligands with Receptors in Vina_en.srt
- 6.42 KB
010 Vina-linux.pl
- 409 B
011 Practical-52 Analysis.mp4
- 11.95 MB
011 Practical-52 Analysis_en.srt
- 2.19 KB
09 - Recent Updates in Structural Biology For MD and Docking
001 Protein Databank Update.mp4
- 46.14 MB
001 Protein Databank Update_en.srt
- 6.31 KB
Bonus Resources.txt
- 386 B
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InfoHash:
AF5D6B0E702BBEFA179120B3FAFEE6C6F68FD7D9
Last updated:
Nov 26, 2022
File count:
262 B
File Category:
9
Tags:
Udemy, Bioinformatics, IT & Software, Other, Tutorials
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Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.pdf
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Jan 4, 2019
42.83 MB
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15
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Biotechnology and Bioinformatics Advances and Applications for Bioenergy, Bioremediation and Biopharmaceutical Research
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Jan 4, 2019
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Python Programming for Biology Bioinformatics and Beyond
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Jan 6, 2019
35.06 MB
1
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Bioinformatics Data Skills - Reproducible and Robust Research with Open Source Tools - 1st Edition (2015) (Pdf, Epub & Mobi) Gooner
Ebook/Course
Jan 5, 2019
32.05 MB
1
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9
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