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Welcome to Chime SquareTM
(www.chimesquare.com), 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.
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.
Use a compatible
browser for your platform. Netscape
Communicator is recommended. Mozilla and NC 7.0 appear to work well and maintain
the remote control as the front window for most operations.
The files have been gzipped to reduce
network traffic times. Large structures are denoted with an asterisk
in the tables.
Structures will load automatically
when you open the page and there will be a series of buttons
available to view selected features. PDB ID codes are listed
with each structure.
Page layouts and structures have been
optimized for a monitor screen resolution of 800 x 600.
Structures (and features) have been
modified for use with a separate resizable remote control window
(indicated by "rc" in the tables). The remote control
window automatically closes when you leave each structure page.
If you do not have Chime installed
or are using an incompatible browser, a static image (.gif) of
the structure should appear.
Biochemistry
and Molecular Biology Home Page