Molecular Docking using Autodock 4.2.6
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Molecular docking software Autodock 4.2.6 is presented. It is free and credible for predicting optimal bound conformations of ligands to proteins. The steps for using Autodock include: (1) preparing the ligand and target protein, (2) optimizing a grid map, (3) selecting docking parameters, (4) running the docking simulation, and (5) analyzing the results. Autodock Tools (ADT) is used for preparation of files in .pdbqt format before docking with Autodock 4.
![5. Running Docking
Start menu / Run âŚ.. cmd.exe
Command lines:
cd folder name/ path
autogrid4 âp grid.gpf [-l grid.glg]
autodock4 âp dock.dpf [-l dock.dlg]](https://image.slidesharecdn.com/autodock-slideshare-170501121446/85/Molecular-Docking-using-Autodock-4-2-6-10-320.jpg)
Molecular Docking using Autodock 4.2.6
- 1. Molecular DockingMolecular Docking using Autodock 4.2.6using Autodock 4.2.6 ⢠Presented by/ Mariam Abdelrasoul Teaching assistant Medicinal Chemistry Department - Faculty of Pharmacy - Assiut University
- 2. AutoDock A software for predicting the optimal bound conformations of ligands to proteins developed by the Scripps institute of technology A software for docking Why AutoDock? Free Credibility Why not? Command lines, no user friendly interface in all steps Lengthy steps
- 3. A ligandA ligand TargetTarget Grid /Grid / docking sitedocking site Autodock Tools, ADT âŚ.pdbqt âŚ.pdbqt âŚ.gpf DockingDocking parametersparameters âŚ.dpf Autodock 4 DockingDocking âŚ.dlg Same folder aS autogri d and autodoc
- 4. Installation of AutoDock Autodock Tools, ADT Autodock 4 AutoDock 4.2, Linux AutoDock 4.2.3, Windows / Cygwin AutoDock 4.2.5, 4.2.6 Windows only ď Autodock vina http://autodock.scripps.edu/
- 5. Steps: 1. Preparation of ligand 2. Preparation of target 3. Grid map optimization 4. Selection of docking parameters 5. Running docking 6. Analysis of results ADT Autodock 4
- 6. Ligand / Input / Open 1. Preparation of ligand Draw and save as mol2 or pdb file Ligand / Output âŚ.. ligand.pdbqt
- 7. ďŹ2.Preparation of target File / OpenâŚâŚâŚâŚâŚ. XXXX.pdb Edit / Charges / Add kollman charges / Compute Gasteiger Edit / Hydrogens / Add polar Save âŚâŚâŚâŚ. Edit / Delete water molecules (β-adrenergic receptor and carazolol, 2rh1.pdb)
- 8. 3. Grid map optimization (2 methods) Grid / Macromolecule / Choose⌠Save as target.pdbqt Grid / Set map type / Choose ligand .pdbqt Grid / Grid boxâŚâŚ parameters File / close saving current Grid / Output / Save gpf âŚâŚ Grid.gpf
- 9. 4. Selection of docking parameters Docking / Macromolecule / Set rigid filename Docking / Ligand / Choose Docking / Search parameters / Genetic algorithm Docking / Docking parameters Docking / Output / LamarckianâŚ. Docking.dpf
- 10. 5. Running Docking Start menu / Run âŚ.. cmd.exe Command lines: cd folder name/ path autogrid4 âp grid.gpf [-l grid.glg] autodock4 âp dock.dpf [-l dock.dlg]
- 11. 6. Analysis of results Analyse / Docking / Open âŚâŚ.. .dlg Analyse / Conformations / PlayâŚ. show conformations Analyse / Clusterings / Show Analyse / Macromolecule / Choose
- 12. Thank you