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--- opthitlead [2013/10/09 08:35] – rkiss
+++ opthitlead [2013/10/09 08:36] – rkiss
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 **__[[usecases|Go back to use cases >>]]__**
-====== Generate new ideas and eliminate problematic parts by 1-Click Scaffold Hop ======
-Scaffold hopping is about finding novel active ligands structurally different from a reference ligand (query). Scaffold hopping can be particularly useful during lead optimization to generate new ideas or to eliminate particular parts of your hit/lead to fix IP, toxicity, selectivity or pharmacokinetic issues. 1-Click Scaffold Hop is searching different subsets of **[[purchasable|Purchasable compounds]]**
-that might be structurally different but share pharmacophore properties with those of the query.
-. Go to **[[http://mcule.com/apps/1-click-scaffold-hop|LEAD OPTIMIZATION / 1-CLICK SCAFFOLD HOP]]**
-. Depending on your **[[http://mcule.com/pricing|Price plan]]**, you can choose from input collections with different sizes
-. Specify your existing hit / lead / reference ligand (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey)
-. Click on **"SCAFFOLD HOP"**
-. After the calculation finishes you can find a number of diverse scaffolds that have similar pharmacophore properties as your query
-. Click on **"VISUALIZE SIMILARITY"** to understand why the two compounds are similar. Corresponding parts are marked with different colors.
-. Remember that all displayed hits are purchasable. To order any of them, click on the orange **"QUOTE"** buttons.
-. You can check your previous 1-Click Scaffold Hop results and queries **[[http://mcule.com/apps/1-click-scaffold-hop/history|HERE]]**. If you run out of storage, check the **[[http://mcule.com/pricing|Price Plans]]** to upgrade.
-. You can use the other Lead Optimization tools, such as **[[http://mcule.com/apps/1-click-docking|1-Click Docking]]**, **[[http://mcule.com/apps/property-calculator|Property Calculator]]** and **[[http://mcule.com/apps/toxicity-checker|Toxicity Checker]]** to further characterize the newly identified scaffolds
-**__[[usecases|Go back to use cases >>]]__**
-====== Property calculator ======
-ADMET properties heavily depend on physicochemical properties. For example, high logP (> 5) and molecular weight (> 500 g/mol) are typically associated with unsuitable ADMET profile. Property calculator creates a physicochemical property profile for your compound in seconds. You can reject compounds with unsuitable logP, insufficient number of H-bond acceptors/donors, too many rotatable bonds, etc.
-. Go to **[[http://mcule.com/apps/property-calculator|LEAD OPTIMIZATION / PROPERTY CALCULATOR]]**
-. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey)
-. Click on **"CALCULATE"**
-. Check the calculated properties of your original hit/lead. Depending on your **[[http://mcule.com/pricing|Price Plan]]**, you might see **Basic** as well as **Advanced** properties. Notice if there are properties in unsuitable/unacceptable ranges (e.g. too high logP).
-. Go back and draw a slightly modified version of your hit/lead
-. Click on **"CALCULATE"**
-. After the calculation finishes you can check the individual properties and see if problematic properties got improved due to your modification in the hit/lead structure
-. You can use the other Lead Optimization tools, such as **[[http://mcule.com/apps/1-click-docking|1-Click Docking]]** and **[[http://mcule.com/apps/toxicity-checker|Toxicity Checker]]** to make sure other properties of the ligand are not impaired. In fact, try to improve multiple things simultaneously by checking all properties of the same idea.
-**__[[usecases|Go back to use cases >>]]__**
-====== Toxicity checker ======
-Certain structural elements of a molecule can be responsible for toxicity. In fact, some substructural motifs occur more frequently in toxic compounds than in non-toxic ones. It therefore makes sense to eliminate such structural motifs from hits/leads as early as possible. Toxicity Checker is based on more than 100 toxic and promiscuous scaffolds. It displays an alert, when such a motif is found, and it displays the incriminated part of the molecule.
-. Go to **[[http://mcule.com/apps/toxicity-checker|LEAD OPTIMIZATION / TOXICITY CHECKER]]**
-. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey)
-. Click on **"CHECK"**
-. If the compound contains any potential toxic substructure, **"FAIL"** message will be displayed along with your structure and the problematic motif in red
-. Go back and try to modify the problematic motif of your hit/lead
-. Click on **"CHECK"**
-. Continue the modifications, until no alert is displayed
-. You can use the other Lead Optimization tools, such as **[[http://mcule.com/apps/1-click-docking|1-Click Docking]]** and **[[http://mcule.com/apps/property-calculator|Property Calculator]]** to make sure other properties of the ligand are not impaired. In fact, try to improve multiple things simultaneously by checking all properties of the same idea.
-**__[[usecases|Go back to use cases >>]]__**