Depth-First

Five Ways to Use PubChem Right Now

By Richard L. Apodaca

You've heard the hype about PubChem, but you're still not convinced. In your mind, the fans have yet to show anything that PubChem does to make your job (which is to get stuff done in the lab) any easier. You've got SciFinder, which does everything you need to do. Why bother with this free Internet thing?

New technologies need to prove themselves. Those that don't simply disappear, or morph into something whose value is more apparent. With these thoughts in mind, here are five things chemists everywhere can use PubChem for right now.

  1. Find the Structure of a Molecule by Name Ever wonder exactly what that drug company in the ad is trying to sell you? If you have the generic (or even brand) name, nine time out of ten, you can find the structure in a few seconds with PubChem. For example, here's the search result for the term "lunesta".
  2. Look up a CAS Number Just about every reagent bottle has a CAS number on it. Sometimes they also have an IUPAC name that's difficult to parse. Maybe you've got a receipt with only CAS numbers and no IUPAC or trivial names. Plug that CAS number into PubChem and you're likely to get the structure quickly and conveniently.
  3. Stop Drawing Molecules - Use a CID Instead Molecular structures are strange beasts. They can't be put into ordinary spreadsheet tables, don't travel well though email, and are a pain to draw in notebooks and reports. PubChem assigns all of its molecules a simple, short number called a Compound Identifier (CID). For example, the CID for lunesta is 969472. This CID does play well with email, spreadsheets, on Webpages, and anywhere else you might want to track chemical information. Because PubChem is a free service, you know you'll always be able to make the CID->structure conversion.
  4. Browse and Search Supplier Catalogs With the recent announcement of Sigma-Aldrich's addition of 56,000 compounds, it's a safe bet that sooner or later, every supplier will upload their compound collection into PubChem. PubChem lets you search by supplier, or even limit your results to particular suppliers. This lets you conveniently search multiple suppliers from a single Web interface.
  5. Link, That Ye May Be Found This one's a bit more out there. With PubChem's march toward becoming the world's compound registration system comes great possibilities. For example, every compound in the PubChem system can be accessed through a homepage. In the case of Lunesta, that page is here. Knowing that a Web page from another site links to PubChem's Lunesta page says some very important things about that site's contents, without much effort from the site's author. Following backlinks, as they're called, is the magic that enables services like Technorati and Google to makes sense of the Web. The next time you're blogging and refer to a compound, try linking to its PubChem page. You may find yourself listed at the top of a structure search without even trying.