BIOL368/F16:Week 8: Difference between revisions
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* This week we will begin to learn how to analyze protein structures. For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein. | * This week we will begin to learn how to analyze protein structures. For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein. | ||
* Chapter 2: Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition). The example worked through in the book uses the sequence of an enzyme called dUTPase. Follow the book example yourself, but instead of investigating dUTPase, use the HIV gp120 envelope protein instead. | |||
* Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition). The example worked through in the book is the epidermal growth factor receptor. Work through this example using the HIV gp120 envelope protein instead. | * Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition). The example worked through in the book is the epidermal growth factor receptor. Work through this example using the HIV gp120 envelope protein instead. | ||
** Swiss-Prot is now part of what is known as the [http://www.uniprot.org UniProt Knowledgebase (UniProt KB)]. UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases. The user interface to this protein database has undergone many revisions since this book was published, but all of the same information can still be found. | ** Swiss-Prot is now part of what is known as the [http://www.uniprot.org UniProt Knowledgebase (UniProt KB)]. UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases. The user interface to this protein database has undergone many revisions since this book was published, but all of the same information can still be found. | ||
Revision as of 09:59, 18 October 2016
This page is currently under construction.
This journal entry is due on Tuesday, October 25 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.
Background for HIV Structure Project
- BEDROCK HIV Problem Space
- HIV Database at Los Alamos National Laboratory
- StarBiochem
- Download NCBI Cn3D
- NCBI Structure Database
References
Reviews
- Merk, A., & Subramaniam, S. (2013). HIV-1 envelope glycoprotein structure. Current opinion in structural biology, 23(2), 268-276. DOI: 10.1016/j.sbi.2013.03.007
- Turner, B. G., & Summers, M. F. (1999). Structural biology of HIV. Journal of molecular biology, 285(1), 1-32. DOI: 10.1006/jmbi.1998.2354
Primary Research Articles for Journal Club
- Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-AIDS drug design. Journal of Biomolecular Structure and Dynamics, 27(2), 179-193. DOI: 10.1080/07391102.2009.10507308
- Kirchherr, J. L., Hamilton, J., Lu, X., Gnanakaran, S., Muldoon, M., Daniels, M., ... & Musonda, R. M. (2011). Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology, 409(2), 163-174. DOI: 10.1016/j.virol.2010.09.031
- Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659. DOI: 10.1038/31405
Individual Journal Assignment
- Store this journal entry as "username Week 8" (i.e., this is the text to place between the square brackets when you link to this page).
- Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Link to this assignment from your journal entry.
- Don't forget to add the "BIOL368/F16" category to the end of your wiki page.
Academic Honesty
As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.
Acknowledgments
In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).
- You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
- I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
- Sign this statement with your wiki signature.
- I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
- Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
- If you copied
wiki syntaxor a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below). - You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."
References
- In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
- data
- facts
- images
- documents, including the scientific literature
- The references in this section should be accompanied by in text citations on your page that refer to these references.
- The references should be formatted according to the APA guidelines.
- For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
- Store your journal entry in the shared BIOL368/F16:Class Journal Week 8 page. If this page does not exist yet, go ahead and create it.
- Link to the shared journal entry from your user page; this should be part of your template.
- Link the shared journal page to this assignment page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "BIOL368/F16" category to the end of the wiki page (if someone has not already done so).
Reflection
- After working with the protein tools on today's assignment, compare your experience with working with the nucleic acid tools versus the protein tools. Which do you like better, and why?
