05.3 Zinc15

5.3 Zinc15

Zinc15 (https://zinc15.docking.org/substances/home/) is an online database where you can search for compounds to be used in virtual screening. The compounds come in ready-to-dock format with their 3D conformations details available for download.

You can search the Zinc database by substructure, text search, similarity search etc. just as with other online databases.

You can draw in the basic structure you would like to search with, or alternatively can upload a file from your computer (i.e. a cdx file from ChemDraw). Once you have selected the options you wish to search with on the right, you can search the database by clicking on the highlighted “search with” button, and then selecting the type of search you wish to perform in the drop-down menu. Here we searched the database by substructure.

This will take you to the next screen where you can view all of the compounds found from your search.

You can filter your dataset, search the catalogue, or simply download the whole list of compounds as a single sdf file. Here Zinc has found 100 compounds currently displayed, we have downloaded this dataset and saved it as an sdf file.

You can then open this sdf file in DataWarrior for further analysis and filtering. The benefit of using Zinc is that compounds already come with their 3D structural information included in the sdf file so you do not need to generate these 3D conformations yourself in other programmes. The sdf downloaded from Zinc could be used directly for docking experiments (however it is advisable that you refine your dataset first).