Differences

This shows you the differences between two versions of the page.

--- 1clickdocking [2013/02/25 15:30] – [Docking protocol] rkiss
+++ 1clickdocking [2013/02/25 15:39] – [Docking protocol] rkiss
@@ Line 28: / Line 28: @@
 **1. Conversion of input ligands defined by mcule IDs, SMILES or InChI strings to 2D MOL**
-mcule ID input: The [[Regsys|mcule structure registration system]] automatically associates 2D MOL files with mcule IDs, therefore 2D MOL files can be easily retrieved.
+mcule ID input: the [[Regsys|mcule structure registration system]] automatically associates 2D MOL files with mcule IDs, therefore 2D MOL files can be easily retrieved.
 SMILES input: SMILES string is first converted to canonical SMILES and then to 2D MOL file by [[http://ggasoftware.com/opensource/indigo|Indigo]]. Next we generate a canonical SMILES from the 2D MOL file and check if the two generated canonical SMILES are identical. In case of a mismatch, the ligand is skipped.
@@ Line 60: / Line 60: @@
 -U “None” (no clean-up)
-**6. Docking with [[http://vina.scripps.edu/|AutoDock Vina]]**
+**6. Docking**
-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 discarded.
+Docking calculations are carried out by [[http://vina.scripps.edu/|AutoDock Vina]] with default parameters. The best four docking poses are stored. To ensure that the identity of the molecule is not modified during docking InChI strings of the input ligand and output conformer are compared and in case of InChI mismatch, the results are discarded.