March 29, 2001

Web review: Links for Linux and chemistry

Author: JT Smith

- by Tina Gasperson -
There is a ton of software designed for use by chemists and other scientists, that runs on Linux. I'm not kidding. OK, maybe not a ton. But if you put it all on CDs and weighed it, it'd be quite substantial. How's that for scientific?Linux and Chemistry isn't the only site of its ilk -- but it is the most logically done and easy-to-read-and-navigate that I've seen. Here, the selections are sorted according to their function and then alphabetized. There's biology, computational, database, graphics, molecular, spectroscopy, and the catch-all "other."

Each section has summaries and links to dozens of titles. In the "molecular" section, for example, there's DOCK -- it explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together. Sounds like it would be fun to play with.

Being a visually-oriented person, I found several good goof-off time candidates under the graphics section. Like CACTVS, a visualization package for chemists, with a full-featured 2D structure editor -- whatever that is. That, and Cn3D, a 3D molecular structure viewer that allows you to "visualize and rotate structure data entries."

Then there's Chemtool, which is a program for drawing organic molecules. Reminds me of seventh grade when I had a fascination with organic chemistry and would sit around sketching out molecule structures when I was supposed to be listening to the teacher talk about ... well, I don't know what he was talking about because I wasn't listening. Anyway, now I can relive my fascination digitally.

Under database, something called GeneMine caught my eye. It says that its the "first expert bioinformatics data mining system to automatically query independent sources." Hmm. Is that the scientist's version of NewsVac? Unfortunately, when I tried to visit the site, it was just a placeholder page.

Even though Linux in Chemistry is the best site of its kind that I've found, it is not without faults -- bad links is the worst one. Someone needs to go through and weed out the 404s. It is disappointing to find what looks like an interesting, download-worthy application, click on the link, and get nothing.

Another shortcoming is the short list of chemists under the chemists section. There's only one, Mathieu Didier, with just a couple of sentences and a link to an email address. Come on! If you're going to create a section especially for chemists who use Linux, make it worth looking at.

The links section is short also, and the first one I clicked on, "Steven's Linux Home Page," was a "not found" one.

To end on a good note, the site is searchable, so if there's a scientific application you've heard of but can't find anywhere, Linux and Chemistry might be a good place to look.

If you know of a great site you think we should review, share it with us.

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