Exercises: The Internet/World Wide Web.

Call up/start the program the Internet Explorer.

1) Once the CWRU-Med School home page is up ( http://mediswww.meds.cwru.edu/ ), follow the links to the Department of Physiology and Biophysics. Find yourself in the student list = that’s the place of your future home page.
Further down, you'll find Pranav Dalals home page. Visit it and set a bookmark (add to Favorites) , so that you can return to this page more easily!

2) Go to the Indians home page, and check the information on yesterday's game.
(You'll find a link on Pranav's home page).
Afterwards, go back to the Departmental Home page.

3) Check out my departmental web pages (What proteins do I work on?). Go to and set a bookmark at my lab home page.

4) Go to the CWRU-home page - follow the computing -software links to find out the information/software to dial-up to the university network, how to get connected etc.

5) Go to Yahoo (www.yahoo.com) or use the search button, and Yahoo your way to the Louvre . Find out, when their most(?) famous painting was painted and by whom?

6) Hit the search button: Use the white pages (www.whowhere.com) and find the home address and telephone number of Marius Clore.

Also note on the result page: you can get directions, even maps at various scales to find the place.

7) Find out Marius’ work phone-number; he works at the National Institutes of Health (NIH).

8) While you are there (at the NIH home page), checkout the post-doc or student fellowships from the NIH: where do you find them?
(Research Training!)

9) Open the location of the Physiology newsgroup?  (Go  - read news)
Any info?
Try the Cell biology or Biophysics newsgroup.

10)  Checkout the bio.software group. Here you finally find a) less spam and b) real questions and help!
Is it difficult to translate the protein sequence back into a DNA sequence? 
Did Anthony find some help/software for this task?

 Close the newsreader window.
 

  (This is a good place for a break, but I guess most of you want to continue to get out of her early.)

For most of the following tasks you'll find links from my lab home page. Among them is a compilation of Bio-sciences related resources on the web, called Pedros' Research tools.

11) Start the Browser, go to the links page from my home page, and open the location of the protein sequence database (called PIR). Look up the sequence of the "antifreeze protein Type II". Load the sequence and save it locally on the desktop with Word, or any text editor available. Then, delete the sequence numbers, any titles etc so that you have only the amino acid sequence. Save that file.

12) Go to Pedro's Molecular Biology tools. Use the Find button/option to a secondary structure-prediction page/location (such as nnpredict, PSSP). You can use PredictProtein (very good site) or PHD; these are e-mail based predictions and you will get the answer several hours later (but it’s a better prediction!). Open the PSSP location and paste the sequence. Remove the sequence numbers (if you haven't already), choose SSP as prediction method and submit the prediction. You'll get a computational prediction on what structural preferences the different regions in the amino acid sequence have. Check the prediction for b-sheet and alpha helical regions, and save the file / or better paste it into your word/sequence/result file. Repeat the same with nnpredict. Do you get the same or at least a similar prediction?

13) Choose Tmpred to get a prediction for trans-membrane helices. Save the result.

14) Again from Pedro’s page, link to a  Blast search server. If the one at the ncbi (National Center for Bioinformatics) is too busy, try some others such as France Blast with Entrez and SRS). Paste the sequence in, (delete sequence numbers). You can leave the spaces in there, (and you don’t need specific or FASTA style headers). Choose blastp search for proteins and submit. Do you find proteins with similar sequence stretches, so-called sequence homologies or similarities? Are there reoccuring protein types, which could indicate that these proteins are evolutionary or in term of their sequence related?

15) Limit the search to proteins of known tertiary structure by changing the search base from nr (non-redundant sequence database) to pdb (Protein structure coordinate database at Brookhaven).

Still hits for the same protein class? Note down the (protein database) accession code (such as 1kde) of one of the higher scoring experimental structures.

16) Connect to the Protein structure database (pdb) database web-site (a link is on Pedro's page, too,). Choose  the 3D browser, or type in the accession code at the main level. Enter the accession code under ID and submit. Get the header only, and paste it into the results file.
To get the entire coordinates (and not only the header of the structure entry, use the save-to disk  and save as a pdb/txt file on the desktop.

Follow the link to install Rasmol, (windows 95 version).  Download the program and execute/start it. Open the coordinate / pdb-file to view the structure you downloaded. Check out how to rotate the molecule, how to change the display (lines, cpk (atom presentation) etc.

Note that you could also give your browser the capability of displaying/rotating molecules. Under the Rasmol-link on the PDB page, there are also links to Chime (which is downloaded and installed in less than 10 minutes).  This is a "plug-in", an added program package which is activated whenever needed, and displays/rotates various views on molecules.  (Please, do not install those on the machines here).

17) Do a Medline literature search via the web. For that go back to my lab home page, choose Medline.

Search for antifreeze+protein. Limit your hits by looking for "structure", and retrieve only the interface between these two searches (29 entries). Look for a structural model of the Type II antifreeze protein. Save that reference in the results file.
Also, look up the abstract for the Houston et al. reference.  The "JBC online button" gives you full access to the entire article (follow it). You can even download the print version (PDF) at the top, and print it locally, saving yourself the photocopying (don't need to do that!).

18) E-mail me your results from today's exercises (the word file you saved as an e-mail, or appended to an e-mail). If you desire, include comments on the browsing/the Web surfing or the exercises in general if you have. (frank@pout.phol.cwru.edu).
Clean up: close all programs, delete the file(s) on the desktop and the Rasmol program you installed.  Have a good weekend.