ZINC-22:Select chemical space for docking

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.