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usecase1cd [2013/12/02 23:15] sanmark more detailed introducted |
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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]]. | 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]]. | ||
| - | 1. 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) | |
| - | 2. 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"** | |
| - | 3. 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 | |
| - | 4. 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. | |
| - | 5. 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. | |
| - | 6. 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. | |
| - | 7. Click on **"DOCK"** | + | |
| - | + | ||
| - | 8. 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. | + | |
| - | + | ||
| - | 9. 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. | + | |
| - | + | ||
| - | 10. 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. | + | |
| - | + | ||
| - | 11. 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. | + | |
| - | + | ||
| - | 12. 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 >>]]__** | **__[[usecases|Go back to use cases >>]]__** | ||
usecase1cd.txt · Last modified: 2013/12/02 23:25 by sanmark
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