1clickdocking
Differences
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1clickdocking [2013/02/25 15:28] – [Docking protocol] rkiss | 1clickdocking [2013/02/25 15:34] – [Docking protocol] rkiss | ||
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SMILES input: SMILES string is first converted to canonical SMILES and then to 2D MOL file by [[http:// | 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:// | + | InChI input: only standard InChIs are accepted. 2D MOL files are generated with [[http:// |
**2. Generation of defined stereoisomers** | **2. Generation of defined stereoisomers** | ||
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**3. Conversion of ligand 2D SDF to 3D SDF** | **3. Conversion of ligand 2D SDF to 3D SDF** | ||
- | Conversion is carried out by OpenBabel. 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** | **4. Conversion of ligand 3D SDF to PDBQT** | ||
- | Input ligands | + | Input ligands |
**5. Preparation of docking targets** | **5. Preparation of docking targets** | ||
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-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.txt · Last modified: 2024/04/09 09:55 by rkiss