Differences

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--- opthitlead [2013/10/09 08:35] – rkiss
+++ opthitlead [2013/10/09 08:35] – rkiss
@@ Line 17: / Line 17: @@
 **__[[usecases|Go back to use cases >>]]__**
-====== Optimize binding affinity and selectivity with 1-Click Docking ======
-Molecular docking simulations predict the binding orientation and affinity of a ligand to a target.
-. Go to **[[http://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, InChI or InChIKey)
-. Select or upload a target
-. Click on **"DOCK"**
-. 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"**
-. 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 **[[http://mcule.com/apps/property-calculator|Property Calculator]]** 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.
-. 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.
-**__[[usecases|Go back to use cases >>]]__**
 ====== Generate new ideas and eliminate problematic parts by 1-Click Scaffold Hop ======