docking_vina
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docking_vina [2012/05/26 21:41] – [Molecular Docking] rkiss | docking_vina [2012/07/29 08:57] – rkiss | ||
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=== Docking (Vina) filter of mcule === | === Docking (Vina) filter of mcule === | ||
- | Docking tool: AutoDock | + | Docking tool: [[http:// |
In the mcule Docking (Vina) filter you can: | In the mcule Docking (Vina) filter you can: | ||
- | - upload | + | - select |
+ | * select from among ~10,000 PDB structures | ||
+ | * search for PDB ID, Protein name, Organism name, UniProt Name/ | ||
+ | * automatic preparation involves: adding hydrogens if none exists in input file; adding Gasteiger charges; merging charges and removing non-polar hydrogens, lone-pairs, water molecules and non-standard residues | ||
+ | * automatic preparation is done by AutoDockTools | ||
+ | * centre of the binding site is automatically determined based on the position of the co-crystallized ligand | ||
+ | - upload target structure (will be available soon) | ||
* target structures can be uploaded in pdb, pdbqt or mol2 files by clicking on " | * target structures can be uploaded in pdb, pdbqt or mol2 files by clicking on " | ||
* uploaded files can be selected for docking | * uploaded files can be selected for docking | ||
- | - automatically prepare your target | + | |
- | * preparation is done by AutoDockTools (version 1.5.6rc3) | + | |
- | * automatic preparation involves: adding hydrogens if none exists in input file; adding Gasteiger charges; merging charges and removing non-polar hydrogens, lone-pairs, water molecules and non-standard residues | + | |
- select the X, Y, Z binding site coordinates (AutoDockTools can help to identify the centre of the binding site of your target) | - select the X, Y, Z binding site coordinates (AutoDockTools can help to identify the centre of the binding site of your target) | ||
- select the binding site area (default is 22 Angstroms) | - select the binding site area (default is 22 Angstroms) | ||
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=== Docking protocol === | === Docking protocol === | ||
- | The uploaded | + | Target structures selected from sc-PDB or uploaded |
=== Analysis of the docking results === | === Analysis of the docking results === | ||
- | The output of the Docking (Vina) filter is a collection of conformers. It includes the generated binding poses of the successfully docked molecules. Docking score is displayed in both list and table views by default. The docking score of AutoDock | + | The output of the Docking (Vina) filter is a collection of conformers. It includes the generated binding poses of the successfully docked molecules. Docking score is displayed in both list and table views by default. The docking score of Vina is a (very rough) estimation of the binding affinity. More negative docking scores suggesting higher affinity. |
=== Example input file for Docking (Vina) === | === Example input file for Docking (Vina) === | ||
- | For testing the Docking (Vina) functionality you can use the following prepared pdbqt file: | + | For testing the Docking (Vina) functionality you can either select a target structure from the filter itself, or use the following prepared pdbqt file: |
[[http:// | [[http:// |