faq
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| faq [2013/01/13 19:28] – sanmark | faq [2013/01/13 19:37] – sanmark | ||
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| Compounds, structures, conformers and products are the currently available entry types that a collection can contain. These different entry types store different level of information. Compounds are tautomer and protonation state independent. Structures represent molecules in a specific tautomer and protonation state. Conformers are structures with 3D coordinates. Products are compounds with associated chemical supplier data. If a workflow step is running on or outputs entries at a different entry level than those in the input collection, the entry level changes. For example, the input collection for Docking(Vina) might contain structures, but since the output is a set of conformers (binding poses), the output collection will contain conformers. To learn more about the different entry levels, click here (link to regsys, entry levels). | Compounds, structures, conformers and products are the currently available entry types that a collection can contain. These different entry types store different level of information. Compounds are tautomer and protonation state independent. Structures represent molecules in a specific tautomer and protonation state. Conformers are structures with 3D coordinates. Products are compounds with associated chemical supplier data. If a workflow step is running on or outputs entries at a different entry level than those in the input collection, the entry level changes. For example, the input collection for Docking(Vina) might contain structures, but since the output is a set of conformers (binding poses), the output collection will contain conformers. To learn more about the different entry levels, click here (link to regsys, entry levels). | ||
| - | //**What is the difference between “Search” and “Screen” tabs. Why are they separated? | + | //**What is the difference between “find chemicals” and “workflow builder” tabs. Why are they separated? |
| - | Under the “Search” tab you can run simple searches ([[exactsearch|Exact]], | + | Under the “find chemicals” tab you can run simple searches ([[exactsearch|Exact]], |
| - | Under the “Screen” tab more complex, multistep virtual screens can be built and run. Available tools under the Screen | + | Under the “workflow builder” tab more complex, multistep virtual screens can be built and run. Available tools under the workflow builder |
| //**Who can see my search/ | //**Who can see my search/ | ||
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| //**How do I set the screening database? | //**How do I set the screening database? | ||
| - | Click on “Input collection” at the top under the “Search” or “Screen” tabs. | + | Click on “Input collection” at the top under the “find chemicals” or “workflow builder” tabs. |
| //**How can I upload my own molecules? | //**How can I upload my own molecules? | ||
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| //**What is a collection? | //**What is a collection? | ||
| - | Collections are fundamental units of the mcule system. They can serve as input for the searches and screens (e.g. Purchasable compounds collection). The results of any searches or screens are collections themselves, users can use such result collections as input for further searches and screens. To learn more about the collections, | + | Collections are fundamental units of the mcule system. They can serve as input for the searches and screens (e.g. [[purchasable|Purchasable compounds collection]]). The results of any searches or screens are collections themselves, users can use such result collections as input for further searches and screens. To learn more about the collections, |
| //**I can't add molecules to my molecule collections. Why?**// | //**I can't add molecules to my molecule collections. Why?**// | ||
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| //**I need to find novel inhibitors of a protein. How should I start?**// | //**I need to find novel inhibitors of a protein. How should I start?**// | ||
| - | There are several ways of doing this. Here is one general example. Go to “Screen”, set a “Property filter” (RO5 max 1). If there is a reference ligand available that is a known inhibitor of your protein, you can use it as a query molecule for “FTrees Visual Similarities” or “Similarity search”. If there is an available crystal structure for your protein, you can check if it can be selected from the ~10,000 prepared target structures in the Docking (Vina) workflow step. To make sure you don’t exceed your limits, use the “Sampler filter” or “Diversity selection” to reduce the number of molecules to the required number. Click on “Screen” to run your screening workflow. The results will be displayed as they are generated. To export the results click on “Export”, | + | There are several ways of doing this. Here is one general example. Go to “workflow builder”, set a “Property filter” (RO5 max 1). If there is a reference ligand available that is a known inhibitor of your protein, you can use it as a query molecule for “FTrees Visual Similarities” or “Similarity search”. If there is an available crystal structure for your protein, you can check if it can be selected from the ~10,000 prepared target structures in the Docking (Vina) workflow step. To make sure you don’t exceed your limits, use the “Sampler filter” or “Diversity selection” to reduce the number of molecules to the required number. Click on “Screen” to run your screening workflow. The results will be displayed as they are generated. To export the results click on “Export”, |
| //**I want to check if a compound is purchasable, | //**I want to check if a compound is purchasable, | ||
| - | To check the on stock amounts of the available products for a compound, you can go to the index page of the compound and click on the " | + | To check the on stock amounts of the available products for a compound, you can go to the [[indexpages|index page]] of the compound and click on the " |
| If you want to order the compound, click on the orange " | If you want to order the compound, click on the orange " | ||
faq.txt · Last modified: 2024/04/09 08:33 by rkiss