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dockingvina [2014/01/01 21:47]
flack [How to use]
dockingvina [2014/03/29 21:58]
flack [Limits]
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 You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://​autodock.scripps.edu/​resources/​adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation,​ only a quick check for file validity will be performed. You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://​autodock.scripps.edu/​resources/​adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation,​ only a quick check for file validity will be performed.
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 +Please note that the PDB upload file size limit is currently 2MB. If you have a larger PDB file, we suggest to extract and upload only the binding site or a single monomer/​chain from the PDB file. You can extract monomers by any text editors. To reduce the file size, you can eliminate all lines and keep the ATOM records only. You can find the chain identifier after the three letter residue name (in the below example "​PRO"​ is the residue and "​A"​ is the chain identifier).
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 +{{:​pdbextr.png?​500|}}
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 == Binding site center == == Binding site center ==
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 ===== Limits ===== ===== Limits =====
  
-The Docking (Vina) filter available in the [[freepackage|Free package]] is limited to 500 input molecules per month. If you need more, [[subscriptionpackages|subscribe]] to our Docking (Vina) package.+The Docking (Vina) filter available in the [[freepackage|Free package]] is limited to 10000 input molecules per month. If you need more, [[subscriptionpackages|subscribe]] to our Docking (Vina) package.
  
 ===== Docking protocol ===== ===== Docking protocol =====
  
 Docking (Vina) workflow step requires input ligands with a valid 3D structure, therefore the input ligand collection is prepared for docking as follows. 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. Molecules failed to dock are skipped. To ensure that molecule conversions did not affect the identity of the molecule, InChI strings of the docking input and output are compared and in case of InChI mismatch, the molecule is skipped. Docking (Vina) workflow step requires input ligands with a valid 3D structure, therefore the input ligand collection is prepared for docking as follows. 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. Molecules failed to dock are skipped. To ensure that molecule conversions did not affect the identity of the molecule, InChI strings of the docking input and output are compared and in case of InChI mismatch, the molecule is skipped.
dockingvina.txt · Last modified: 2014/03/29 21:58 by flack