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.

old text - might be something worth saving?

Step 3. Select database subset. Large scale docking can be used to query enormous areas of chemical space, however it can be helpful to narrow down the search range for economic and time purposes. ZINC-22 [Tingle, 2022] can be selected using the 3D tranche browser of cartblanche22.docking.org. Navigate to cartblance22.docking.org, select “Tranches->3D” from the pulldown menu This page allows you to select any subset of chemical space you would like. There are a number of helpful predefined categories which can be selected using the menu button at the top right of the browser. For example, the “small leads” category selects molecules with heavy atom count from 17-19. Once your selection has been made, click the download button at the top right of the browser. Under “Method”, change file type to DOCK37 db2.tgz, and URLs to AWS S3. Confirm the download. This file will serve as your database subset for docking.