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usecaseligbased [2013/10/11 10:39]
rkiss
usecaseligbased [2013/12/04 21:19]
sanmark use ordered list
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 Ligand-based virtual screening does not utilize the 3D structure of the target when searching for new hits. Instead, it is based on the structure of a reference ligand (endogenous ligand, known inhibitor, etc.) that binds to a target and/or exhibits some beneficial effect. In ligand-based virtual screening, compounds are typically ranked based on the similarity to the reference ligand (query). Ligand-based virtual screening does not utilize the 3D structure of the target when searching for new hits. Instead, it is based on the structure of a reference ligand (endogenous ligand, known inhibitor, etc.) that binds to a target and/or exhibits some beneficial effect. In ligand-based virtual screening, compounds are typically ranked based on the similarity to the reference ligand (query).
  
-1. Go to **[[https://​mcule.com/​search/​screen/?​template=ligand-based-virtual-screening|HIT IDENTIFICATION / LIGAND-BASED VIRTUAL SCREEN]]** +  - Go to **[[https://​mcule.com/​search/​screen/?​template=ligand-based-virtual-screening|HIT IDENTIFICATION / LIGAND-BASED VIRTUAL SCREEN]]** 
- +  ​- ​Select the input collection if other than all **[[purchasable|Purchasable compounds]]** of the Mcule database 
-2. Select the input collection if other than all **[[purchasable|Purchasable compounds]]** of the Mcule database +  ​- ​The loaded template workflow includes a number of individual workflow steps that will be executed sequentially on the input collection. You can adjust the parameters of the individual workflow steps. Detailed description of the available workflow steps and their parameters can be found **[[tools|HERE]]**. 
- +  ​- ​Specify your query for the **[[similaritysearch|"​Similarity search"​]]** (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) 
-3. The loaded template workflow includes a number of individual workflow steps that will be executed sequentially on the input collection. You can adjust the parameters of the individual workflow steps. Detailed description of the available workflow steps and their parameters can be found **[[tools|HERE]]**. +  ​- ​Try and set different property ranges in the **"​Basic property filter"​** step. Click on **"+ ADD CONDITION"​** to add another **"​Condition"​**,​ and click on the **"​X"​** button next to a **"​Condition"​** to remove it. 
- +  ​- ​You can also add new workflow steps by clicking on the **"ADD WORKFLOW STEP"​** button on the right at the end of the workflow. Detailed description of the available workflow steps can be found **[[tools|HERE]]**. 
-4. Specify your query for the **[[similaritysearch|"​Similarity search"​]]** (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) +  ​- ​After finalizing your workflow, you can set the **"​Name"​** and **"​Description"​** of the output collection and the **"​Maximum hits"​**. If you don't want to limit the number of hits in the output, you can delete the number from this field. Note that the maximum number of molecules in a single collection is limited and it depends on your **[[https://​mcule.com/​pricing/​|Price Plan]]**.. 
- +  ​- ​Click on **"​RUN"​** 
-5. Try and set different property ranges in the **"​Basic property filter"​** step. Click on **"+ ADD CONDITION"​** to add another **"​Condition"​**,​ and click on the **"​X"​** button next to a **"​Condition"​** to remove it. +  ​- ​Results will be generated and displayed on-the-fly 
- +  ​- ​After the calculation is finished, the hits will be ranked by the last workflow step (if you did not add new steps to the template workflow, they will be rank ordered by the similarity scores) 
-6. You can also add new workflow steps by clicking on the **"ADD WORKFLOW STEP"​** button on the right at the end of the workflow. Detailed description of the available workflow steps can be found **[[tools|HERE]]**. +  ​- ​You can request quote for any of the hits by clicking on the orange **"​QUOTE"​** buttons next to them. You can request quote for all hits in the output collection by clicking on the orange **"​QUOTE"​** button in the top right corner. Alternatively,​ you can select only the most interesting hits by using the checkboxes on the left and add them into a new or an already existing collection (**"​ADD TO"** button). After that you can go to **"​COLLECTIONS"​**,​ open your created collection and click on the orange **"​QUOTE"​** button in the top right corner.
- +
-7. After finalizing your workflow, you can set the **"​Name"​** and **"​Description"​** of the output collection and the **"​Maximum hits"​**. If you don't want to limit the number of hits in the output, you can delete the number from this field. Note that the maximum number of molecules in a single collection is limited and it depends on your **[[https://​mcule.com/​pricing/​|Price Plan]]**.. +
- +
-8. Click on **"​RUN"​** +
- +
-9. Results will be generated and displayed on-the-fly +
- +
-10. After the calculation is finished, the hits will be ranked by the last workflow step (if you did not add new steps to the template workflow, they will be rank ordered by the similarity scores) +
- +
-11. You can request quote for any of the hits by clicking on the orange **"​QUOTE"​** buttons next to them. You can request quote for all hits in the output collection by clicking on the orange **"​QUOTE"​** button in the top right corner. Alternatively,​ you can select only the most interesting hits by using the checkboxes on the left and add them into a new or an already existing collection (**"​ADD TO"** button). After that you can go to **"​COLLECTIONS"​**,​ open your created collection and click on the orange **"​QUOTE"​** button in the top right corner.+
  
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usecaseligbased.txt · Last modified: 2014/01/01 16:50 by flack