Differences

This shows you the differences between two versions of the page.

--- usecase1cd [2013/12/02 22:15] – more detailed introducted sanmark
+++ usecase1cd [2013/12/02 22:25] (current) – use order list sanmark
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 Molecular docking simulations predict the binding orientation and affinity of a ligand to a target. With [[1clickdocking|1-Click Docking]] you can run sequential docking simulations online, and optimize the binding affinity of your ligand. A step-by-step description is provided here for this use case. If you would like to get more information about the [[1clickdocking|1-Click Docking]] application, [[1clickdocking|please click here]].
-. Go to **[[https://mcule.com/apps/1-click-docking/|LEAD OPTIMIZATION / 1-CLICK DOCKING]]**
+  - Go to **[[https://mcule.com/apps/1-click-docking/|LEAD OPTIMIZATION / 1-CLICK DOCKING]]**
+  - Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES or InChI)
-. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES or InChI)
+  - Select or upload a target
+  - Click on **"DOCK"**
-. Select or upload a target
+  - After the docking calculation finishes you can check the estimated binding affinity (docking score - more negative means higher affinity) and visualize the critical interactions that have been formed between your ligand and the target by clicking on **"VISUALIZE POSE"**.
+  - Go back and draw a slightly modified version of your hit/lead
-. Click on **"DOCK"**
+  - Click on **"DOCK"**
+  - After the docking calculation finishes you can compare the docking scores and the formed interactions of the modified molecule and those of the original hit/lead.
-. After the docking calculation finishes you can check the estimated binding affinity (docking score - more negative means higher affinity) and visualize the critical interactions that have been formed between your ligand and the target by clicking on **"VISUALIZE POSE"**.
+  - To get an idea where the compound can be further adjusted, take a closer look at the binding mode (**"VISUALIZE POSE"**). Turn on the **"proteinsurface"** feature to see where is additional space for optimization. Red colored surface parts indicate polar regions.
+  - Continue testing new ideas and improve the docking scores. You can also run other Lead Optimization tools, such as **[[https://mcule.com/apps/property-calculator/|Property Calculator]]** and **[[https://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.
-. Go back and draw a slightly modified version of your hit/lead
+  - You can check your previous 1-Click Docking results and queries **[[http://mcule.com/apps/1-click-docking/history|HERE]]**. If you run out of storage, check the **[[http://mcule.com/pricing|Price Plans]]** to upgrade.
+  - Additionally, you can take a step forward and calculate the binding affinity to off-targets, you don't want your ligand to bind to. For example to design a subtype specific inhibitor, you might need high binding affinity to subtype "A", but low affinity to subtype "B". For this select other targets and dock your ligand again.
-. Click on **"DOCK"**
-. After the docking calculation finishes you can compare the docking scores and the formed interactions of the modified molecule and those of the original hit/lead.
-. To get an idea where the compound can be further adjusted, take a closer look at the binding mode (**"VISUALIZE POSE"**). Turn on the **"proteinsurface"** feature to see where is additional space for optimization. Red colored surface parts indicate polar regions.
-. Continue testing new ideas and improve the docking scores. You can also run other Lead Optimization tools, such as **[[https://mcule.com/apps/property-calculator/|Property Calculator]]** and **[[https://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.
-. You can check your previous 1-Click Docking results and queries **[[http://mcule.com/apps/1-click-docking/history|HERE]]**. If you run out of storage, check the **[[http://mcule.com/pricing|Price Plans]]** to upgrade.
-. Additionally, you can take a step forward and calculate the binding affinity to off-targets, you don't want your ligand to bind to. For example to design a subtype specific inhibitor, you might need high binding affinity to subtype "A", but low affinity to subtype "B". For this select other targets and dock your ligand again.
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