Biochemistry is visual and biochemists rely heavily on the ability to depict biomolecules. You will also notice that biochemists use a different shorthand notation than most chemists. For example, biochemists often leave most of the hydrogen atoms off of molecular structures.
This is a listing of web resources that may be useful for students.
Reviews:
Access to the Primary Literature:
Structures
There are a number of programs that display biochemical molecules in three dimensions and permit you to rotate them on the computer screen. About ten percent of the population (the instructor included) can't see the three dimensional images produced by two pictures on a page and the plastic glasses. Everyone with sight, even people with one eye, can visualize the shape of molecules rotating on a computer screen. Programs are available for both Macintosh and PC computers.
Cn3D is great! You can use images downloaded from an internet browser, or it can act as a stand-alone downloader. It can also do simple sequence comparisons. It is, however, a memory hog. The program takes at least 12 (and prefers 24) Meg of memory. If you are going to use it while running Netscape, plan on 64 Meg minimum. If you are going to use it as a stand-alone program, you may be able to use a machine with less.
RasMol is pretty good. It uses less resources than Cn3D. You can download structural files with your browser and either configure the browser to open RasMol to view them, or open RasMol separately and view the files.
To access structural files that you can view in Cn3D or RasMol try the Entrez Structure site. This will permit you to search the protein data base (PDB) for structures of the molecule of interest. If you just type in something simple like 'DNA' or 'lysozyme' you will receive many hits, so you may want to use more specific search strings. Clicking on an entry will give you a page that will permit you to download either a Cn3D or RasMol file. Your browser can be configured to open these programs so that the files can be viewed immediately, or you can save the file and open it later.
In the chemistry courses developed here, we use Jmol to display three-dimensional structures.
