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usecase1cd [2013/10/10 16:08] – flack | usecase1cd [2013/12/02 22:25] (current) – use order list sanmark | ||
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====== Optimize binding affinity and selectivity with 1-Click Docking ====== | ====== Optimize binding affinity and selectivity with 1-Click Docking ====== | ||
- | Molecular docking simulations predict the binding orientation and affinity of a ligand to a target. | + | 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, |
- | 1. Go to **[[https:// | + | - Go to **[[https:// |
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- | 2. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) | + | |
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- | 3. Select or upload a target | + | |
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- | 4. Click on **" | + | |
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- | 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 **" | + | |
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- | 6. Go back and draw a slightly modified version of your hit/lead | + | |
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- | 7. Click on **" | + | |
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- | 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. | + | |
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- | 9. To get an idea where the compound can be further adjusted, take a closer look at the binding mode (**" | + | |
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- | 10. Continue testing new ideas and improve the docking scores. You can also run other Lead Optimization tools, such as **[[https:// | + | |
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- | 11. You can check your previous 1-Click Docking results and queries **[[http:// | + | |
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- | 12. Additionally, | + | |
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usecase1cd.txt · Last modified: 2013/12/02 22:25 by sanmark