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--- dockingvina [2013/01/14 08:53] – sanmark
+++ dockingvina [2014/03/29 20:58] (current) – [Limits] flack
@@ Line 19: / Line 19: @@
 Docking results are ranked by docking scores (the more negative the better), which indicates how well the ligand is predicted to bind to the target. It is, however, also important to check the binding mode and analyze whether it is in agreement with a priori knowledge.
-Since docking is one of the most computationally intensive drug discovery tools, it is highly recommended to apply it in the last steps in a screening workflow. [[mculepropertyfilter|mcule property filter]], [[reos|REOS filter]] and [[diversitysel|Diversity selection]] might be used to narrow down the search space to apply the Docking (Vina) step to the most interesting candidates only.
+Since docking is one of the most computationally intensive drug discovery tools, it is highly recommended to apply it in the last steps in a screening workflow. [[basicpropertyfilter|basic property filter]], [[reos|REOS filter]] and [[diversitysel|Diversity selection]] might be used to narrow down the search space to apply the Docking (Vina) step to the most interesting candidates only.
 ==== Options ====
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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.
+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).
+{{:pdbextr.png?500|}}
 == Binding site center ==
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 ===== 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 (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.