1clickdocking
Differences
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Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
1clickdocking [2013/02/25 15:34] – [Docking protocol] rkiss | 1clickdocking [2013/10/09 13:40] – [Docking protocol] sanmark | ||
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**1. Conversion of input ligands defined by mcule IDs, SMILES or InChI strings to 2D MOL** | **1. Conversion of input ligands defined by mcule IDs, SMILES or InChI strings to 2D MOL** | ||
- | mcule ID input: | + | mcule ID input: |
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:// | ||
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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.txt · Last modified: 2024/04/09 09:55 by rkiss