132 A Practical Guide to Cancer Systems Biology
Procedure
I. Navigate to PubChem by using its URL (https://pubchem.ncbi.
nlm.nih.gov/) or by querying the search engine (e.g., Google).
II. Do search according to the ligand information you have (Fig. 2(a)).
If you have some keywords about the ligand, do searching directly in
the search box and click the “Go” button.
If you have more information about the ligand (e.g., molecular weight
range, hydrogen bond acceptor count, etc), go to advanced search page
by clicking the “advanced” link on the right side of the “Go” button,
fill the blanks and hit “Search” button in the advanced search page.
If you have the ligand structure, click “structure search” on the right
panel, go to structure search page, fill your structure and select the
searching method (e.g., similarity search, identity search, substructure
search, or superstructure search), then hit “Search” button.
III. No matter which way you choose to do your query, you will be taken to
the result page. View the results carefully (Fig. 2(b)).
If your goal is a specific compound, please go through the list one by one
by going into the detail page. You may download the structure by using
“Download→2D structure” or “Download→3D conformers” in the
detailed page. After you finish your download, take note of PubChem
CID of this compound for future reference (Fig. 2(c)).
If you want to grab all compounds that fit into your query, please find
“Structure Download” button under “Actions on your results” section
in the search result list. Saving in SDF format is recommended. Don’t
forget to take note of your query date (Fig. 2(d)).
- Get ligand structures from ZINC
Here we will guide you to query ZINC^8 and download your query result into
a ligand database (Fig. 3). Please note that you may download only up to
1000 molecules at once by using this method.
Materials
- Information of your ligands. For example, you should know the name
of the ligand, to which they are similar, or molecular weight range
and so on.