1clickdocking
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1clickdocking [2013/02/25 15:39] – [Docking protocol] rkiss | 1clickdocking [2024/04/09 09:55] (current) – rkiss | ||
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- | ====== 1-Click Docking | + | ====== 1-CLICK DOCKING |
// | // | ||
**[[http:// | **[[http:// | ||
- | {{: | + | {{: |
- | Docking predicts the binding orientation and affinity of a ligand to a target. [[https:// | + | Docking predicts the binding orientation and affinity of a ligand to a target. [[https:// |
===== When to use ===== | ===== When to use ===== | ||
- | When you are looking for the binding mode or docking score of a particular ligand, [[https:// | + | When you are looking for the binding mode or docking score of a particular ligand, [[https:// |
===== How to use ===== | ===== How to use ===== | ||
- | [[https:// | + | [[https:// |
===== Results ===== | ===== Results ===== | ||
- | {{: | + | {{: |
The best binding poses are listed together with their docking scores. More negative values indicate higher binding affinity. Binding poses can be displayed (" | The best binding poses are listed together with their docking scores. More negative values indicate higher binding affinity. Binding poses can be displayed (" | ||
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Unknown or undefined tetrahedral stereocenters and cis-trans double bonds are converted into well-defined centers and double bonds by the stereoisomer generator of mcule. | Unknown or undefined tetrahedral stereocenters and cis-trans double bonds are converted into well-defined centers and double bonds by the stereoisomer generator of mcule. | ||
- | **3. Conversion of ligand 2D SDF to 3D SDF** | + | **3. Conversion of ligand 2D MOL to 3D MOL** |
- | Conversion is carried out by [[http:// | + | Conversion is carried out by [[http:// |
- | **4. Conversion of ligand 3D SDF to PDBQT** | + | **4. Conversion of ligand 3D MOL to PDBQT** |
Input ligands are converted to pdbqt format by using [[http:// | Input ligands are converted to pdbqt format by using [[http:// | ||
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-A “None” (do not make any repairs) | -A “None” (do not make any repairs) | ||
+ | |||
-C (preserve input charges ie do not add new charges) | -C (preserve input charges ie do not add new charges) | ||
+ | |||
-U “None” (no clean-up) | -U “None” (no clean-up) | ||
1clickdocking.1361806740.txt.gz · Last modified: 2013/02/25 15:39 by rkiss