Welcome to Chime SquareTM, the site for three dimensional molecular graphics! The assembled collection of molecular structures are intended to facilitate your understanding of the relationship between structure and function of macromolecules. To accomplish this, the viewer (you) should have (or be developing) a foundation in biochemistry (proteins and enzymes), organic chemistry, and inorganic chemistry.
I would encourage you to use Protein Explorer (and Protein Comparator) and some of the other applications that have been developed by Eric Martz at the University of Massachusetts. Swiss-PdbViewer (Deep View) and RasMol are also very good resources for protein structure analyses. You may want to visit Gale Rhode's site for a thoughtful discussion. This is a very effective method to learn about macromolecule structure and function.
|Protein Explorer (Protein Comparator)|
|Swiss-PdbViewer (Deep View)|
Protein structures may be obtained from the Protein Data Bank (PDB), which is hosted by the Research Collaboratory for Structural Bioinformatics.
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The protein data bank. Nucleic Acids Research 28:235-242.
Requirements and Notes:
|Citric acid cycle||Oxidative stress|
|Oxidative phosphorylation||Copper proteins|
|Proteins & DNA||Manganese proteins|
|Nucleic acids||Molybdenum proteins|
|Transcription factors||Zinc proteins|
The following animations have as an additional requirement the installation of the Macromedia Shockwave plugin.
|Ester formation between ethanoic acid and methanol|