Chem 406 Web Termpapers - Fall 2002
Web Termpaper Assignment
The Assignment:
You are assigned the task of writing a web-based term paper on the DNA binding protein that you chose from the list. The term paper should be a minireview that deals with the structure-function of this DNA binding protein. The primary incentive behind making this term paper is to provide you with the ability to illustrate your term paper with interactive three-dimensional molecular models using the Chime plug-in. It will also allow you to embedded buttons that when pushed will modify the Chime models. The web format will allow us to publish your efforts for world-wide consumption. Keep in mind, the content of your paper will be the primary factor used in evaluating it. Using interactive three-dimensional molecular models produced using the Chime plug-in is currently one of the best ways of communicating information about macromolecular structures to large audiences. During the construction of your Web term paper, it is hoped you will learn something about the structure-function relationship of your protein so that you can communicate this knowledge to others. Specific items that you should include in your term paper include:
- A description of the role played by your class of DNA binding protein
- A description of the specific interactions that your protein makes with DNA and the significance of these interactions for the protein in carrying out its role.
- You should do an exhaustive search of the Protein Data Bank for all relavent structures and discuss the range of structures that are currrently available for study towards understanding the role of your protein. You should be come familiar with the range of search tools available for the Protein Data Bank.
- As part the descriptions of your DNA binding protein you should use Chime and embedded buttons to provide a description of secondary, tertiary and, if present, the quaternary structure of you protein
- As part the description of your DNA binding protein's physiological role, you should use Chime and embedded buttons to provide a discription of the specific interactions that your protein makes with DNA.
- Points to remember when creating your web site:
- Any image files you include in your web site should be either gif or jpeg files with a resolution of 72 dpi. Do not use images with resolutions higher than 150 dpi. Adobe PhotoShop is available in the Philllips 468 and in most of the GA computer labs and can be used to touch-up graphics files.
- You will need to use a Netscape 4.x browser to view your site. You should alert visitors to you site of this fact and point them to sites where they can obtain both Netscape and the Chime browser plug-in.
Literature Resources:
Your paper should draw from between 7 to 10 references. These should be references to scienific articles, not web sites. You shouild submit copies of the articles that you reference along with your website. Resources for developing a set of references include:
- The NIH's National Center for Biotechnology Information (NCBI) provides free online access to PubMed which you can use to do a key word searchs of the scientific literature.
- The Science & Engineering subject guide listing at the McIntyre library web page provides links to the full text of The American Chemical Society Journals, which includes Biochemistry, and the index BIOSIS.
- Science Citation Index: This extremely useful research tool allows you to find scientific articles which have cited a particular article of interest. For example, the PDB file for a protein provides the reference for the article in which a structure was first reported in the literature. You can use that citation in a Science Citation Index search to find other articles that refer to this article.
- CAS-Online is the online version of Chemical Abstracts. If you would like to do a CAS-Online search of the literature, see me.
- Journal Web Sites
- Other Related Sites
Web Page Development Resources:
- The 1996 , 1997, 1998, 1999, 2000 and 2001 Chem406 Web term papers.
- UW-Eau Claire Web Development Tools Site
- The Molecules in Cyberspace Tutorial on embedding Chime and JavaScript buttons tutorial. This tutorial provides a step-by-step lesson on how to embed Chime models along with interactive buttons into web pages.
- The Oxymyoglobin site is an example of using Chime with embedded scripts to describe the structure-function relationships of the oxygen storage protein, oxymyoglobin. This site provides an example of how to use script files to store the button scripts.
- The Interactive Biochemistry site provides some elaborate examples, that were produced by Charles Grisham at the University of Virginia, for using Chime with embedded scripts to describe structure-function relationships for a wide range of biological macromolecules. This site contains some nice examples of how Chime along with embedded buttons can be used to illustrate a discussion on enzyme mechanisms. To see how they constructed their pages, click on the frame contianing the text with buttons and select Page Source from Netscape's View menu. You will need a username and password to use this site (Hint: protein structures)
- The Chime plug-in. This browser plug-in should already be installed on the computers in the General Access labs. The plug in only works reliably with Netscape's 4.x browsers. It was developed by MDL, Inc. and you can download a free copy of the plug-in from their site. Alternatively, you can download a copy of the plug-in from the Chem406_F01_Lab folder on the BMBServer. The most recent version of the plug-in is version 2.6.
- Rasmol is a standalone molecular modeling application that works similarly to Chime. It is a very useful tool for creating and testing button scripts. Rasmol is available in the General Access computer labs. You can also download a free copy of the application from the Chem406_F01_Lab folder on the BMBServer. You should use version 2.7.2.1.
- MDL's Chime Tutorials. MDL is the company that develops and distributes Chime.
- Attributes for the Chime embed tag. This is a pdf file that can be displayed and printed with Acrobat Reader.
- Additional Script commands. These are script commands, in addition to the Rasmol commands, which work only with Chime. They include the "Move" command that is demonstrated in the Oxymyoglobin site. This is a pdf file that can be displayed and printed with Acrobat Reader.
- The Rasmol/Chime site at the University of Massachusetts provides a wide range of resources for using Rasmol and Chime.
![[UWEC Web]](../Media/smuwec.gif)
[Chemistry Dept.] [Chem 406]
Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu
updated: Wednesday, January 8, 2003