1clickdocking
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1clickdocking [2013/02/25 14:49] – [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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===== Docking protocol ===== | ===== Docking protocol ===== | ||
- | 1. Conversion of input ligands defined by mcule IDs, SMILES or InChI strings to 2D SDF | + | **1. Conversion of input ligands defined by mcule IDs, SMILES or InChI strings to 2D MOL** |
- | To ensure that molecule conversion did not affect | + | mcule ID input: |
- | 2. Generation of defined stereoisomers | + | SMILES input: SMILES string is first converted to canonical SMILES and then to 2D MOL file by [[http:// |
+ | |||
+ | InChI input: only standard InChIs are accepted. 2D MOL files are generated with [[http:// | ||
+ | |||
+ | **2. Generation of defined stereoisomers** | ||
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 (OpenBabel) | + | **3. Conversion of ligand 2D MOL to 3D MOL** |
- | To ensure that molecule conversions did not affect the identity of the molecule, InChI strings of the input ligand and output conformer are compared and in case of InChI mismatch, the results are not displayed. If the conformer generation fails due to InChI mismatch, another defined stereoisomer is generated in step 2 (if possible). | + | Conversion is carried out by [[http:// |
- | 4. Conversion of ligand 3D SDF to PDBQT (AutoDockTools) | + | **4. Conversion of ligand 3D MOL to PDBQT** |
- | 5. Preparation of docking targets (AutoDockTools) | + | Input ligands are converted to pdbqt format by using [[http:// |
- | Nearly 10,000 target structures integrated from the [[http:// | + | **5. Preparation of docking targets** |
+ | |||
+ | Nearly 10,000 target structures integrated from the [[http:// | ||
[-e]: delete every nonstd residue from any chain | [-e]: delete every nonstd residue from any chain | ||
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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) | ||
- | 6. Docking | + | **6. Docking** |
- | To ensure that molecule conversions did not affect | + | Docking calculations are carried out by [[http:// |
1clickdocking.1361803797.txt.gz · Last modified: 2013/02/25 14:49 by rkiss