faq
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| faq [2012/10/18 08:43] – szferi | faq [2014/01/06 10:47] – flack | ||
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| //**Will my previous searches deleted? | //**Will my previous searches deleted? | ||
| - | We won’t delete any of your search/ | + | We won’t delete any of your search/ |
| //**Where can I access my previous search results? | //**Where can I access my previous search results? | ||
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| //**How many molecules can be stored in a single collection? | //**How many molecules can be stored in a single collection? | ||
| - | The Free package | + | The [[freepackage|Free package]] contains a maximum 10,000 entry limit for each of your collections. However, if you subscribe to any for-fee packages, you will be able to create collections of any size. Note: when executing a screening workflow, the collection limit only affects the size of the last, saved collection, i.e. the number of molecules passing from one to another workflow step is not limited. |
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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/ | ||
| - | By default, all your collections are private, which means that no one except you can get access to your search/ | + | By default, all your collections are private, which means that no one except you can get access to your search/ |
| //**Is the data transfer between our site and mcule secured? | //**Is the data transfer between our site and mcule secured? | ||
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| //**How can I get access to extra searching/ | //**How can I get access to extra searching/ | ||
| - | Extra tools, like FTrees Visual Similarites or ChemAxon Properties are provided on a subscription basis. To get access to these tools, go to our Pricing page (link). Subscriptions can be purchased by just a few clicks. To learn more about our subscription packages, click here (link to subscription) | + | Extra tools, like FTrees Visual Similarites or ChemAxon Properties are provided on a subscription basis. To get access to these tools, go to our [[https:// |
| //**I’m working at XY University. Can I get a discount for the subscription packages? | //**I’m working at XY University. Can I get a discount for the subscription packages? | ||
| - | Yes. Typically different prices are applied for all subscription packages. To see the acedemic prices go to our Pricing page (link) | + | Yes. Typically different prices are applied for all subscription packages. To see the acedemic prices go to our [[https:// |
| //**I’m interested in your subscription packages, but I couldn’t find the right package options that would perfectly suit my needs. Can you offer me a special package? | //**I’m interested in your subscription packages, but I couldn’t find the right package options that would perfectly suit my needs. Can you offer me a special package? | ||
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| //**The status of my search/ | //**The status of my search/ | ||
| - | This is a very rare event, but it might be possible that we encounter an “Error” during your search/ | + | This is a very rare event, but it might be possible that we encounter an “Error” during your search/ |
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| //**What databases can be screened at mcule.com? | //**What databases can be screened at mcule.com? | ||
| - | The mcule database is a set of high quality molecules that have been processed by the rigorous molecule registration system of mcule. The Purchasable compounds collection | + | The mcule database is a set of high quality molecules that have been processed by the rigorous molecule registration system of mcule. The [[purchasable|Purchasable compounds collection]] contains more than 4 million compounds that are available for purchase. This is set by default as input collection for your searches and screens. Other collections (made public by other mcule users) can be also set as input collection. We also plan to introduce further collections in near future: |
| //**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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| //**What export formats are available? | //**What export formats are available? | ||
| - | Collections can be exported as SDF, SMILES, InChI, InChIKey and mcule ID. Contact us, if you need any other file types. To learn more about collection export, click here (link to collection export). | + | Collections can be exported as SDF, SMILES, InChI, InChIKey and mcule ID. Contact us, if you need any other file types. To learn more about [[collexport|collection export]]. |
| //**Why do I need to register to start using mcule?**// | //**Why do I need to register to start using mcule?**// | ||
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| //**If I register, do I have to pay for anything? Is mcule free?**// | //**If I register, do I have to pay for anything? Is mcule free?**// | ||
| - | You don’t need to pay anything for registration. It is free. After registration you will get immediate access to the Free package | + | You don’t need to pay anything for registration. It is free. After registration you will get immediate access to the [[freepackage|Free package]]. [[subscriptionpackages|Subscription packages]] are also available for extra tools and features. |
| //**Will the currently freely available features and tools remain free forever? | //**Will the currently freely available features and tools remain free forever? | ||
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| //**How can I order compounds? | //**How can I order compounds? | ||
| - | To order a single compound, go to its index page (click on its 2D representation or its mcule ID) and click on the orange “Quote” button on the right. To order a collection of compounds, open the collection and click on the orange “Quote” button on the right. For more information about the ordering process, click here (link to delivery). | + | To order a single compound, go to its index page (click on its 2D representation or its mcule ID) and click on the orange “Quote” button on the right. To order a collection of compounds, open the collection and click on the orange “Quote” button on the right. For more information about the ordering process, click [[delivery|here]]. |
| //**How can I make sure I won't use all my credits for docking with a single screen?**// | //**How can I make sure I won't use all my credits for docking with a single screen?**// | ||
| - | You can use filters before docking to reduce the number of molecules. We recommend to use Property | + | You can use filters before docking to reduce the number of molecules. We recommend to use the [[basicpropertyfilter|basic property |
| //**When browsing the results, can I display physchem properties for my hits?**// | //**When browsing the results, can I display physchem properties for my hits?**// | ||
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| //**Where can I find the crystal structure of my target that I could use for docking? | //**Where can I find the crystal structure of my target that I could use for docking? | ||
| - | In the Docking (Vina) workflow step box, you can click on the “Select target” button and select from the ~10,000 prepared target structures (integrated from scPDB(link)). If you can’t find any target structures there, you can check the Protein Data Bank website (www.rcsb.org) and download more target structures in PDB format. These PDB files can be upload by clicking on “Upload a file” in the Docking(Vina) workflow step box. It is recommended to run an automatic preparation on all unprepared PDB files, which can be selected in the “Upload docking target” dialog box. | + | In the Docking (Vina) workflow step box, you can click on the “Select target” button and select from the ~10,000 prepared target structures (integrated from scPDB(link)). If you can’t find any target structures there, you can check the Protein Data Bank website ([[http://www.rcsb.org]]) and download more target structures in PDB format. These PDB files can be upload by clicking on “Upload a file” in the Docking(Vina) workflow step box. It is recommended to run an automatic preparation on all unprepared PDB files, which can be selected in the “Upload docking target” dialog box. |
| //**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”(link) | + | 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”, |
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| //**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 (link) | + | 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 " | ||
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| //**What structure-based and ligand-based tools are available at mcule.com? | //**What structure-based and ligand-based tools are available at mcule.com? | ||
| - | To get a list of the currently available tools and features, click here and check our Pricing | + | To get a list of the currently available tools and features, click [[screen|here]] and check our [[https:// |
| //**I ran a docking calculation on the “Purchasable collection” and there is no product availability information for some of my hits. Why?**// | //**I ran a docking calculation on the “Purchasable collection” and there is no product availability information for some of my hits. Why?**// | ||
| It is possible that some input molecules contained unknown or undefined stereo centers. These cannot be directly processed by docking. Input molecules for Docking (Vina) should have 3D coordinates, | It is possible that some input molecules contained unknown or undefined stereo centers. These cannot be directly processed by docking. Input molecules for Docking (Vina) should have 3D coordinates, | ||
faq.txt · Last modified: 2024/04/09 08:33 by rkiss