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screen [2012/10/12 14:02] – rkiss | screen [2013/12/04 23:17] – [Workflow] rkiss | ||
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- | ====== | + | ====== |
+ | **[[http:// | ||
- | Under the “Screen” tab, linear [[http://en.wikipedia.org/ | + | {{:workflowbuilder.png?700|}} |
- | You can add a name for each workflow (“Name” field at the top). This name will be associated to the screening | + | The mcule technology revolutionizes compound selection either |
+ | ====== When to use ====== | ||
- | You can select on which [[collmanagement|collection]] the screen will be performed in the “Input collection” field. By default, the [[purchasable|“Purchasable compounds collection”]] is set as input collection. Other collections (e.g. public collections or your previously created collections) can be also selected. | + | ==== Virtual screening ==== |
- | The “Maximum hits” field is set to 1,000 by default. If you don't want to limit the number of results, you can delete the number from this field. Note that if you are using the [[freepackage|Free package]], the maximum number of molecules in a single | + | The [[https:// |
- | By default only one workflow step is displayed. You can add more steps by clicking on the “Add workflow step” button, which can always be found under the last added workflow step on the right. The maximum number of workflow steps you can add into a single workflow is 10. The order of the workflow steps is arbitrary, i.e. any step can be put after any other step. However, when building a screening workflow it makes sense to consider at least two aspects: (i) speed and (ii) usage limits of the steps. For example, the [[propertyfilter|Property filter]] is a workflow step with no monthly limits and it can reduce the size of the input collection very quickly, while [[dockingvina|Docking (Vina)]] is more computationally intensive and your allowance of the number of input molecules is limited. We therefore suggest that you put the [[propertyfilter|Property filter]] first and add the [[dockingvina|Docking (Vina)]] step after. Here are some of the available workflow steps ordered by their speed: | + | ==== Library design ==== |
- | [[sampler|Sampler]] > [[exactsearch|Exact search]] > [[bulkexactsearch|Bulk exact search]] > [[propertyfilter|Property filter]] > [[similaritysearch|Similarity search]] > [[substructuresearch|Substructure search]] > [[smartsquery|SMARTS query filter]] > [[reos|REOS filter]] > [[chemaxonpropcalc|ChemAxon calculators]] > [[ftrees|FTrees Visual Similarities]] > [[diversitysel|Diversity | + | You can design screening libraries by filtering the purchasable chemical space based on chemical diversity (large-scale diversity |
- | To move the workflow steps upwards or downwards in a workflow, you can click on the up or down arrows in the upper right corner of each step’s box. If you would like to delete a workflow step, click on the “X” button in the upper right corner of the step box. To display/ | + | ====== How to use ====== |
- | All user-built workflows including the query molecules are saved and can be accessed together with the results by the user at any time. To do this, select the result collection (under the “Collections” tab) and click on “Display query”. Note that your queries and workflows will always be private, even if you change the privacy level of the result collection (they can never be seen by other users). | + | Imagine the [[https:// |
+ | |||
+ | ==== Input ==== | ||
+ | |||
+ | At the top, you can specify the **Input** - these will be the molecules loaded into the funnel. You can select on which [[collmanagement|collection]] the screen will be performed in the " | ||
+ | |||
+ | ==== Workflow ==== | ||
+ | |||
+ | Then you execute different tools and filters in the **Workflow**. With the [[https:// | ||
+ | |||
+ | By default only one workflow step is displayed. You can add more steps by clicking on the "Add workflow step" button, which can always be found under the last added workflow step on the right. The maximum number of workflow steps you can add into a single workflow is 10. The order of the workflow steps is arbitrary, i.e. any step can be put after any other step. However, when building a screening workflow it makes sense to consider at least two aspects: (i) speed and (ii) usage limits of the steps. For example, the [[basicpropertyfilter|basic property filter]] is a workflow step with no monthly limits and it can reduce the size of the input collection very quickly, while [[dockingvina|Docking (Vina)]] is more computationally intensive and your allowance of the number of input molecules is limited. We therefore suggest that you put the [[basicpropertyfilter|basic property filter]] first and add the [[dockingvina|Docking (Vina)]] step after. Here are some of the available workflow steps ordered by their speed: | ||
+ | |||
+ | [[sampler|Sampler]] > [[exactsearch|Exact search]] > [[similaritysearch|Similarity search]] > [[bulkexactsearch|Bulk exact search]] > [[basicpropertyfilter|Property filters]] > [[substructuresearch|Substructure search]] > [[smartsquery|SMARTS query filter]] > [[ftrees|FTrees Visual Similarities]] > [[reos|REOS filter]] > [[chemaxonpropcalc|ChemAxon calculators]] > [[diversitysel|Diversity selection]] > [[dockingvina|Docking (Vina)]] | ||
+ | |||
+ | To move the workflow steps upwards or downwards in a workflow, you can click on the up or down arrows in the upper right corner of each step’s box. Alternatively, | ||
+ | |||
+ | All user-built workflows including the query molecules are saved and can be accessed together with the results by the user at any time. To do this, select the result collection (under the "Collections" | ||
+ | |||
+ | We have prepared a few workflow templates which are good starting points to create your customized workflows: | ||
+ | |||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | |||
+ | |||
+ | ==== Output ==== | ||
+ | |||
+ | At the bottom, you can specify the **Output**, number of hits and name of the output collection. You can add a name for each workflow (" |
screen.txt · Last modified: 2024/04/09 08:34 by rkiss