Chime SquareTM Animations

Molecular Graphics Resource

Eric C. Niederhoffer, Ph.D.

Associate Professor of Biochemistry and Molecular Biology

Southern Illinois University School of Medicine
600 Agriculture Drive, Carbondale, IL 62901-6503
Rm 112 Lindegren, 618-453-6467
Copyright 2000- , E.C. Niederhoffer.
All Rights Reserved. All trademarks and copyrights are the property of their respective owners.

Welcome to Chime SquareTM (, the BMB Online 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.

Macromolecular Structure Applications
 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:

Chime Presentations
 Proteins  More Proteins
 Glycolysis  Dioxygen carriers
 Citric acid cycle  Oxidative stress
 Gluconeogenesis  Cobalt proteins
 Oxidative phosphorylation  Copper proteins
 Photosynthesis  Iron proteins
 Nitrogenase  Iron-sulfur proteins
 Proteins & DNA  Manganese proteins
 Nucleic acids  Molybdenum proteins
 Activators  Nickel proteins
 Repressors  Protein comparison
 Transcription factors  Zinc proteins

The following animations have as an additional requirement the installation of the Macromedia Shockwave plugin.

Chime/Shockwave Animations
 Ester formation between ethanoic acid and methanol


Biochemistry and Molecular Biology Resources

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