usecasestrbased
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Structure-based virtual screening utilizes the 3D structure of the target when searching for new hits. During the screening, predicted 3D structures of small molecules are fitted into the binding site of the experimentally determined or modeled 3D structure of the target (docking calculation). The 3D structures of thousands of large macromolecules have been already determined by X-ray crystallography or NMR spectroscopy and can be easily selected or uploaded in Mcule. Small molecules predicted to form critical interactions with the target get better (more negative) docking scores and are ranked higher. | Structure-based virtual screening utilizes the 3D structure of the target when searching for new hits. During the screening, predicted 3D structures of small molecules are fitted into the binding site of the experimentally determined or modeled 3D structure of the target (docking calculation). The 3D structures of thousands of large macromolecules have been already determined by X-ray crystallography or NMR spectroscopy and can be easily selected or uploaded in Mcule. Small molecules predicted to form critical interactions with the target get better (more negative) docking scores and are ranked higher. | ||
- | 1. Go to **[[https:// | + | - Go to **[[https:// |
+ | - Select the input collection if other than all **[[purchasable|Purchasable compounds]]** of the Mcule database | ||
+ | - The loaded template workflow includes a number of individual workflow steps that will be executed sequentially on the input collection. You can adjust the parameters of the individual workflow steps. Detailed description of the available workflow steps and their parameters can be found **[[tools|HERE]]**. | ||
+ | - Try to set different property ranges in the **" | ||
+ | - Set the target for the **[[dockingvina|" | ||
+ | - You can also add new workflow steps by clicking on the **"ADD WORKFLOW STEP" | ||
+ | - After finalizing your workflow, you can set the **" | ||
+ | - Click on **" | ||
+ | - Results will be generated and displayed on-the-fly | ||
+ | - After the calculation is finished, the hits will be ranked by the last workflow step (if you did not add new steps to the template workflow, they will be rank ordered by the docking scores) | ||
+ | - Check the predicted binding mode of the best hits by clicking on **" | ||
+ | - If there is information available on critical amino acids of your target that participate in ligand binding, check if the hit forms interactions with those residues. | ||
+ | - You can request quote for any of the hits by clicking on the orange **" | ||
- | 2. Select the input collection if other than all **[[purchasable|Purchasable compounds]]** of the Mcule database | + | **__[[usecases|Go back to use cases »]]__** |
- | + | ||
- | 3. The loaded template workflow includes a number of individual workflow steps that will be executed sequentially on the input collection. You can make adjustment in the parameters of the individual workflow steps. Detailed description of the available workflow steps and their parameters can be found **[[tools|HERE]]**. | + | |
- | + | ||
- | 4. Try and set different property ranges in the **" | + | |
- | + | ||
- | 5. Set the target for the Docking (Vina). You can upload a PDB file (3D structural data for your target) or search by keyword and select from ~10,000 prepared target structures. | + | |
- | + | ||
- | 6. You can also add new workflow steps by clicking on the **"ADD WORKFLOW STEP" | + | |
- | + | ||
- | 7. After finalizing your workflow, you can set the **" | + | |
- | + | ||
- | 8. Click on " | + | |
- | + | ||
- | 9. Results will be generated and displayed on-the-fly | + | |
- | + | ||
- | 10. After the calculation is finished, the hits will be ranked by the last workflow step (if you did not add new steps to the template workflow, they will be rank ordered by the docking scores) | + | |
- | + | ||
- | 11. Check the predicted binding mode of the best hits by clicking on **" | + | |
- | + | ||
- | 12. If there is information available on critical amino acids of your target that participate in ligand binding, check if the hit forms interactions with those residues. | + | |
- | + | ||
- | 13. You can request quote for any of the hits by clicking on the orange **" | + | |
- | + | ||
- | **__[[usecases|Go back to use cases >>]]__** | + |
usecasestrbased.1381312242.txt.gz · Last modified: 2013/10/09 09:50 by rkiss