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**[[http:// | **[[http:// | ||
- | {{: | + | {{: |
- | The [[screen|Workflow Builder]] provides a comprehensive set of [[tools|drug discovery tools]] that can be used as LEGO bricks to build up complex workflows. The built workflows can be effectively used for **[[http:// | + | The mcule technology revolutionizes compound selection either |
+ | ====== When to use ====== | ||
- | The mcule technology revolutionizes compound selection by providing powerful, advanced searching and filtering tools in the Workflow Builder. You can design | + | ==== Virtual |
- | Under the “workflow builder” tab, linear | + | The [[https://mcule.com/search/screen/|Workflow Builder]] is well-suited for designing and running virtual screens for **hit identification**. It can be used to run structure-based and ligand-based |
- | You can add a name for each workflow (“Name” field at the top). This name will be associated to the screening workflow as well as to the collection containing the results of the screening workflow. If you leave this field blank, a unique, timestamped name will be generated automatically (e.g. search_2012-10-01_23: | + | ==== Library design ==== |
- | You can select on which [[collmanagement|collection]] | + | You can design screening libraries by filtering |
- | 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 collection is 10,000, which implicitly limits the “Maximum hits” to 10,000. | + | ====== How to use ====== |
- | 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, | + | Imagine |
- | [[sampler|Sampler]] > [[exactsearch|Exact search]] > [[similaritysearch|Similarity search]] > [[bulkexactsearch|Bulk exact search]] > [[mculepropertyfilter|Property filters]] > [[substructuresearch|Substructure search]] > [[smartsquery|SMARTS query filter]] > [[reos|REOS filter]] > [[chemaxonpropcalc|ChemAxon calculators]] > [[ftrees|FTrees Visual Similarities]] > [[diversitysel|Diversity selection]] > [[dockingvina|Docking (Vina)]] | + | ==== Input ==== |
- | To move the workflow steps upwards or downwards in a workflow, you can click on the up or down arrows | + | At the top, you can specify the **Input** - these will be the molecules loaded into the funnel. You can select |
- | 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). | + | ==== 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]] > [[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