Appendix: Some information regarding protein modeling software
Using RasMol, a protein modeling/viewing software package
- http://www.openrasmol.org/. Home page for RasMol and OpenRasMol, a molecular graphics visualization tool. This page was updated in 2002, and refers to RasMol version 2.72. Describes RasMol features, and provides background, but not as straightforward as other RasMol sites (below).
- http://www.umass.edu/microbio/rasmol/getras.htm. Refers to RasMol version 2.6 and 2.7, and mentions an update of home page in 1999. Provides straightforward directions for downloading different versions of RasMol.
- http://www.openrasmol.org/doc/rasmol.html. RasMol 2.73 home page. Updated 2/05. Perhaps more information than a beginner would require.
Modeling software linked to the International protein structure data base
- http://ca.expasy.org/spdbv/. Home page for Deep View and the Swiss Protein Data Base Viewer. The version is 3.7, and the page was updated 3/06. This page has tutorials, and assists you in downloading the modeling software. The DeepView-Swiss-Protein Data Base Viewer is an application that provides a user friendly interface. It allows one to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain. The graphics are “'intuitive” and there is a straightfoward menu interface.
- http://ca.expasy.org/. A home page for all things proteomic. Perhaps has too much information for the beginner. Last modified 4/06. This page has some education links regarding proteins structure. However, the links are for researchers to use, i.e. not geared necessarily to teachers. This url also has links for comparing protein sequences, and more. 3. http://www.parallelgraphics.com/products/cortona/. No specific relevance to protein modeling, this url provides 3-D graphics viewing software that can be used with protein models.
List of sources consulted
This is not complete. For example, I googled something from the additional information on growing Arabidopsis—I was checking to see if whatever it was was a type—and it brought up the Arabidopsis Biological Resource Center at Ohio State, from which the material was apparently copied. The center, which is mentioned in the text for Module 1, is not cited in the list of sources for Module ! and is not credited as being the source of the “additional information.”
Connecticut Academic Performance Test - Second Generation, Science Handbook, Connecticut State Department of Education, 2001 (143 pp.)
“Rapid Homogenization Kit for Plant Leaf DNA Amplification” Instruction Manual. Cartagen Molecular Systems, Seattle, WA.
“DNeasy Plant Mini-Kit” Instruction Manual. Qiagen Inc. Valencia, CA.