ZINC-22:Select chemical space for docking
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This tutorial describes how to use CartBlanche22.docking.org to select chemical space for docking.
Step 1. Think about what you want
- How big is the site? How many atoms can it accommodate in the ligand?
- Charge properties of the binding site: does the site want anions, neutrals, cations?
- Known ligands for the site? What are their properties? Do you want physically similar molecules?
Step 2. Use Cartblanche to make your selection
- Browse to cartblanche22.docking.org and select tranches -> 3D
- Pick the preset closest to what you want. The presets are available in the top right.
- Fine tune your selection. Select charge if you know it.
- Click the download button (top right) and select the format and access method you require.
- download the selection.
For Large Scale Docking, we recommend docking by H?? number. Thus grep H17 ZINC-downloaded-select > h17.aws grep H18 ZINC-downloaded-select > h18.aws and so on.