Illustration: Complexes of Sucrose Octasufate with Fibroblast Growth Factor
Data Source: Protein Data Bank, File: 1AFC.pdb
Some Computer Programs
of Interest
for High School Science
Examples of the use of these programs for some projects at the high school level will be forthcoming.
PCs (Microsoft Operating Systems) such as Windows 7 or XP
a. Swiss PDB viewer - aka DeepViewFairly simple Swiss army knife type program for viewing and analyzing protein structures
A heavier duty program with more functionality and capability than DeepView
A package that provides a Linux like shell that can be used to learn about the Linux operating system as well as to run programs that will not run directly under Windows.
Apple Operating System - OSX
a. Swiss PDB viewer - aka DeepViewFairly simple Swiss army knife type program for viewing and analyzing protein structures
A heavier duty program with more functionality and capability than DeepView
On Apple systems there is no need to install Cygwin as Unix - Darwin flavor - is underneath OSX and a terminal is provided on the operating system from which can be issued Linux commands.
UNIX Operating System - Ubuntu preferred
The use of UNIX will be encouraged in future posts, but for this introduction PC and Apple systems are probably simpler for beginners. If you are adventurous the links above for Swiss PDB viewer and Chimera will also lead you to packages that are suitable for Linux installation. I have been able to run them under Ubuntu 10.x, 11.x, and 12.x systems.
Some information about Ubuntu may be found here. Highly recommended as starter Linux operating system.
(This illustration is from the Ubuntu site. "Get Ubuntu now" link
not functional here. Go to site for actual download.)
If you are starting from ground zero with Ubuntu, I strongly suggest 12.04 (LTD). Versions marked LTD will be supported for five years. Non LTD distros have a much shorter life and constant upgrading becomes an annoyance.
If you run into trouble with installation, please put questions in comments.
Have fun.
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Added 6/15: My favorite structure. Go to the Protein Data Bank link below and I'll bet you can figure out why. More on this important crystal structure in the future.
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Added 6/15: My favorite structure. Go to the Protein Data Bank link below and I'll bet you can figure out why. More on this important crystal structure in the future.
Crystal structure of mitochondrial malate dehydrogenase
First one to identify the four small - red/silver - molecules gets bragging rights and a cite. Clue: it ISN'T malate... Bonus: how did these molecules get here?
Step right up and give your answers in the comment section.
Don't be bashful. Wrong answers will not stay posted, so you don't have to worry about being embarrassed.
Step right up and give your answers in the comment section.
Don't be bashful. Wrong answers will not stay posted, so you don't have to worry about being embarrassed.
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