dockingvina
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dockingvina [2013/01/14 08:38] – sanmark | dockingvina [2014/03/29 20:42] – rkiss | ||
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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. | 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 ==== | ==== Options ==== | ||
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== Upload target == | == Upload target == | ||
- | {{:upload.jpg?500|}} | + | {{:upload.png?500|}} |
You can upload your own target by clicking on “Upload a file”. All uploaded files will remain private and won't be accessible by any other user. | You can upload your own target by clicking on “Upload a file”. All uploaded files will remain private and won't be accessible by any other user. | ||
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You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http:// | You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http:// | ||
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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/ | ||
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+ | {{: | ||
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== Binding site center == | == Binding site center == |
dockingvina.txt · Last modified: 2014/03/29 20:58 by flack