docking_vina
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- | ==== Molecular Docking ==== | ||
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- | Molecular docking is a method that attempts to assess the binding affinity of a ligand to a particular target (protein, DNA, carbohydrates, | ||
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- | Docking mainly consists of the following two steps: (i) pose generation, (ii) affinity prediction (scoring). During pose generation, the ligand is placed into the binding site by sampling its rotational and translational degrees of freedom of the ligand. Subsequently, | ||
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- | === Docking (Vina) filter of mcule === | ||
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- | Docking tool: AutoDock Vina (1.1.2). | ||
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- | In the mcule Docking (Vina) filter you can: | ||
- | - upload target structures | ||
- | * target structures can be uploaded in pdb, pdbqt or mol2 files by clicking on " | ||
- | * 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 binding site area (default is 22 Angstroms) | ||
- | - select the exhaustiveness parameter of conformational sampling (range: 1-8; default: 2) | ||
- | - select the maximum number of conformers to be generated (range: 1-9; default: 1) | ||
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- | === Docking protocol === | ||
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- | The uploaded target structure is prepared for docking by AutoDockTools. If the user choose to opt out the automatic preparation, | ||
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- | === Analysis of the docking results === | ||
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- | 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 Vina is a (very rough) estimation of the binding affinity. More negative docking scores suggesting higher affinity. | ||
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- | === Example input files for Docking (Vina) === | ||
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- | For testing the Docking (Vina) functionality here is a prepared pdbqt file: | ||
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- | [[http:// | ||
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- | Binding center:\\ X: 0.09\\ Y: -14.83\\ Z: 10.43 | ||
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- | Binding site (Angstrom): | ||
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docking_vina.1338065032.txt.gz · Last modified: 2012/05/26 20:43 by rkiss