Journal+Club+Summer+13

To Go: Alyssa, (Kevin+ Nicolet), (Katherine & Marianna), Tony, (Jacky & Kavya), (Young & Grace), Melissa, Stephanie, Renee + ?, Oscar + ?, Madeline
 * Journal Club Presentations/Discussions**

9th Paper Miteva, M. A.; Lee, W. H.; Montes, M. O.; Villoutreix, B. O., Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. //Journal of Medicinal Chemistry// **2005,** //48// (19), 6012-6022.
 * MONDAY 29-July**
 * PRESENTERS: Grace & Young**
 * MitevaVirtualFREDDOCKSurflexJMedChem2005.pdf**


 * COMPLETED PAPERS 2013 Summer:**

1st Paper Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. //Bioorganic & Medicinal Chemistry Letters// 2003, 13 (15), 2493-2496.
 * MONDAY 3-June**
 * NAME**

2nd Paper Park, H.; Kim, Y. J.; Hahn, J. S., A novel class of Hsp90 inhibitors isolated by structure-based virtual screening. //Bioorganic & Medicinal Chemistry Letters// **2007,** //17// (22), 6345-6349.
 * MONDAY 10-June**
 * PRESENTER NAMES: William I and Ramiro R**

3rd Paper Zhang, Y.; White, S.; Rock, C., Inhibiting bacterial fatty acid synthesis. //J Biol Chem// **2006,** //281// (26), 17541-4.
 * MONDAY 17-June**
 * PRESENTER NAMES: Priya & Vicky (The Dynamic Duo)**

4th Paper Cho, Y.; Ioerger, T.; Sacchettini, J., Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. //J Med Chem// **2008,** //51// (19), 5984-92.
 * MONDAY 24-June**
 * PRESENTERS:** **Alyssa**


 * Technical Presentation** by: **Melissa** on PCR

5th Paper Prasannan, P.; Suliman, H. S.; Robertus, J. D., Kinetic analysis of site-directed mutants of methionine synthase from Candida albicans. //Biochem Biophys Res Commun// **2009,** //382// (4), 730-4.
 * MONDAY 1-July**
 * PRESENTERS: Kevin + Nicolet**

6th Paper Herschhorn, A.; Hizi, A., Virtual screening, identification, and biochemical characterization of novel inhibitors of the reverse transcriptase of human immunodeficiency virus type-1. //J Med Chem// **2008,** //51// (18), 5702-13.
 * MONDAY 8-July**
 * PRESENTERS: Katherine & Marianna**
 * JournalClubQuestions072312_HIV.doc**

7th Paper Singh, J.; Chuaqui, C.; Boriack-Sjodin, P.; Lee, W.; Pontz, T.; Corbley, M.; Cheung, H.; Arduini, R.; Mead, J.; Newman, M.; Papadatos, J.; Bowes, S.; Josiah, S.; Ling, L., Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). **Bioorg Med Chem Lett** 2003, 13 (24), 4355-9.
 * MONDAY 15-July**
 * PRESENTERS: Tony**

8th Paper Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K., Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. **Bioorg Med Chem** 2007, 15 (21), 6810-8.
 * MONDAY 22-July**
 * PRESENTERS: Kavya & Jacqueline**

**Potential Papers:**
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. //PLoS Negl Trop Dis// **2011,** //5// (11), e1411.
 * LiWolbachia_ftsz_PLOSNegTropDis2011.pdf**






 * JournalClubQuestions071612HisG.docx**


 * JournalClubQuestions072312_HIV.doc**

Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. //J Biol Chem// **2007,** //282// (27), 19905-16.

Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. //Infect Disord Drug Targets// **2009,** //9// (3), 327-43.

Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. //Nat Rev Microbiol// **2008**, 6 (1), 41-52.

Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.

Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. //Arch Biochem Biophys// **2009,** //483// (1), 23-8.

1st Week: none 2nd Week: 3rd Week: 4th Week: 5th Week: 6th Week - July th: 7th Week - July th: 8th Week - July th: 9th Week - July th:
 * Presentation Order:**


 * Guidelines:**
 * prepare a 10 minute powerpoint slide show
 * __Start__ out with a title slide that has the __Journal Article name__, __Journal Name__ and __Authors__ on it.
 * Put YOUR name on title slide also since you are presenting.
 * Put the __date__ of the presentation on their as well - and something like '**VDS Summer Journal Club**'
 * Create an introduction that provides a broad perspective for the specific __#|work__ being presented. For example, if you are presenting a __#|paper__ on a new protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
 * Include a picture or image that helps give a visual for the background.
 * Include any statistics about the disease and its prevalence (this is motivation)
 * Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any techniques that we are currently using in our lab?
 * __Include graphs and figures from the paper__. Use the **SNIPPING tool** in Windows to get pictures of the graphs, etc. from the paper. However, you will want a few 'original' images of your own. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
 * Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
 * Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
 * Do the results suggest any additional experiments that would be the next__.__?


 * Feel free to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
 * Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
 * <span style="font-family: Arial,Helvetica,sans-serif;">What is the most significant contribution of the specific work to the field in general?
 * <span style="font-family: Arial,Helvetica,sans-serif;">Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Go through your talk at least once as a practice run

Run a **draft** of your presentation by **Dr. B** a few days before you present it. Upload your presentation __before__ class to the **GroupMeetingSlides/GroupMeetingSlides/StudentPresentations** folder on **Google Docs**
 * TIPS:
 * for best contrast and readability - use black text on white background.
 * Put date on the title slide
 * When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
 * For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?