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--- 1clickdocking [2013/02/25 14:26] – rkiss
+++ 1clickdocking [2024/04/09 09:55] (current) – rkiss
@@ Line 1: / Line 1: @@
-====== 1-Click Docking ======
+====== 1-CLICK DOCKING ======
 //**"Molecular docking has never been easier!"**//
 **[[http://www.youtube.com/watch?v=xJicx3sqLpI|WATCH TUTORIAL VIDEO!]]**
-{{:1clickdocking_new.png?800|}}
+{{:1clickdocking_new.png?600|}}
-Docking predicts the binding orientation and affinity of a ligand to a target. [[https://mcule.com/apps/1-click-docking|1-Click Docking]] is the easiest molecular docking solution online.
+Docking predicts the binding orientation and affinity of a ligand to a target. [[https://mcule.com/apps/1-click-docking/|1-Click Docking]] is the easiest molecular docking solution online.
 ===== When to use =====
-When you are looking for the binding mode or docking score of a particular ligand, [[https://mcule.com/apps/1-click-docking|1-Click Docking]] is an ideal solution to start with. It typically gives you good insights about how your ligand can bind to the target: what critical interactions it forms at the binding site. One step forward is to use the [[Dockingvina|Docking (Vina)]] filter and dock multiple ligands into a single target.
+When you are looking for the binding mode or docking score of a particular ligand, [[https://mcule.com/apps/1-click-docking/|1-Click Docking]] is an ideal solution to start with. It typically gives you good insights about how your ligand can bind to the target: what critical interactions it forms at the binding site. One step forward is to use the [[Dockingvina|Docking (Vina)]] filter and dock multiple ligands into a single target.
 ===== How to use =====
-[[https://mcule.com/apps/1-click-docking|1-Click Docking]] is extremely easy to use: draw your input ligand, select your docking target and click on Dock!
+[[https://mcule.com/apps/1-click-docking/|1-Click Docking]] is extremely easy to use: draw your input ligand, select your docking target and click on Dock!
 ===== Results =====
-{{:1clickdockingres_new.png?800|}}
+{{:1clickdockingres_new.png?600|}}
 The best binding poses are listed together with their docking scores. More negative values indicate higher binding affinity. Binding poses can be displayed ("Visualize pose" button) and downloaded ("Download pose" button).
@@ Line 26: / Line 26: @@
 ===== Docking protocol =====
-. 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 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.
+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.
-. Generation of defined stereoisomers
+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.
+InChI input: only standard InChIs are accepted. 2D MOL files are generated with [[http://openbabel.org|OpenBabel]]. Next we generate a new standard InChI from the 2D MOL file and check if the two generated standard InChIs are identical. In case of a mismatch, the ligand is skipped.
+**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.
-. 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://openbabel.org|OpenBabel]] (free and basic plan) or with [[https://www.chemaxon.com/marvin/help/calculations/conformation.html#conformer|ChemAxon's Conformers plugin]]. 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 ligand is skipped. If the conformer generation fails due to InChI mismatch, another defined stereoisomer is generated in step 2 (if possible).
-. Conversion of ligand 3D SDF to PDBQT (AutoDockTools)
+**4. Conversion of ligand 3D MOL to PDBQT**
-. Preparation of docking targets (AutoDockTools)
+Input ligands are converted to pdbqt format by using [[http://autodock.scripps.edu/resources/adt|AutoDockTools]] (prepare_ligand4.py) with default parameters.
-Nearly 10,000 target structures integrated from the [[http://bioinfo-pharma.u-strasbg.fr/scPDB|sc-PDB database]] ([[http://www.ncbi.nlm.nih.gov/pubmed/21398668|Meslamani J, Rognan D, Kellenberger E. Bioinformatics. 2011, 27, 1324-6]]) have been automatically prepared by AutoDockTools using default options, except:
+**5. Preparation of docking targets**
+Nearly 10,000 target structures integrated from the [[http://bioinfo-pharma.u-strasbg.fr/scPDB|sc-PDB database]] ([[http://www.ncbi.nlm.nih.gov/pubmed/21398668|Meslamani J, Rognan D, Kellenberger E. Bioinformatics. 2011, 27, 1324-6]]) have been automatically prepared by [[http://autodock.scripps.edu/resources/adt|AutoDockTools]] (prepare_receptor4.py) using default options, except:
 [-e]: delete every nonstd residue from any chain
@@ Line 50: / Line 56: @@
 Otherwise, PDBQT files are generated by the following options:
--A “None”
+-A “None” (do not make any repairs)
--C
--U “None”
+-C (preserve input charges ie do not add new charges)
+-U “None” (no clean-up)
-. 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.