134 A Practical Guide to Cancer Systems Biology
the bar under the large “ZINC” logo. A small panel will pop up and
showing all possible search methods. Choose the method which fit your
needs most (Fig. 3(a)).
III. Irrespective of the method used, query results will be listed on screen
(Fig. 3(b)).
If you are using quick search and there is only one result (e.g., search
“aspirin” in quick bar), you will be brought into compound detail page
describing that chemical. In this case, just download its structure in this
detail page. (Download options are under the SMILES string) (Fig. 3(c))
IV. Under the bar containing “Search”, “Subsets”, “Help” buttons you can
find a combo box with “Overview” text on it. It is the left of the three
combo boxes. Click on that combo box, browse to “Download” section
and pick the format you like (Fig. 3(b)).
If you wish to filter the result by their purchasability, make your
adjustment by using the rightmost combo box (with “Everything” text
on it by default).
V. After you have done, click the “Refresh” button on the right. The
download will begin soon (Fig. 3(b)).
- Get pre-defined ligand database from ZINC
Here, we will guide you to fetch pre-defined ligand database from ZINC
(Fig. 4).
Materials
- If you are using Microsoft Windows, obtain‘wget’downloader and place
them into a place where it can be located by the operation system.
(i.e., place‘wget’into any directory indicated in‘‘%PATH%’’environment
variable)
Procedure
I. Navigate to official site of ZINC database by using its url (http://zinc.
docking.org/), or search “ZINC database” in your search engine.
II. Move your mouse to “Subsets” button in the bar under the large “ZINC”
logo. You will see a small panel popped up. On that panel, you can see
“By catalog property target ring cart” (four options). You may click in
them and explore to find the subset you need (Figs. 4(a)–(b)).