Sandbox423

This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!

Spring 2015 Chem423 Team ProjectsSpring 2015 Chem423 Team Projects

Understanding the chemical basis of disease and life processes

Follow instructions posted at Student Projects for UMass Chemistry 423 Spring 2015.

Teams, Topics, and LinksTeams, Topics, and Links

1. Emily Friis, Md Shafiul Hossain, Emily Hutchinson, Hieu (Vinny) La, John MacMunn, Kevin Purcell: Protein kinase C related kinase/Tofacitinib (prostrate and ovarian cancer)-4OTI - 4OTI

2. Arash Manafirad, Mahdiyeh Yazdani, Allison Coutu, Jack Caudwell, Christopher Borcoche, Thanh Nguyen, Sonny Nguyen.,Tranthyretin/genistein complex - 3kgt

3. Jacob Kellett, Leah Caffrey, Patrick Harney, Bridget Kilkenny, Brandon Kittredge, Matthew Long topic name - Opioid Receptor 4djh

4. Michael Bresnahan, Matthew Caissy, Jonathan Dullea, James Eyke, Adlina Hasni, Xuanting Wang: Dengue virus methyltransferase bound to a SAM-based inhibitor - 3p8z

5. Nick Barberio, Nicole Garvin, Megan Greiner, Peter Kelly, Charit Tippareddy, John Vetrano: LRRK2/kinase inhibitors: Parkinsons (4py1) - 4py1

6. Ashley Andrews, Steven Ayotte, Lee Johnson, Deanna Oliveira, Seo Yeon Orite, Mark Allen Pagkaliwangan: Pim-1 kinase/aminooxadiazoleindole inhibitor(cancer) (4ty1) - 4ty1

7. Colin Hannahan, Megi Marina, Cassandra Martin, Eric Rice, Benjamin Ryter, Matthew Tuttle MTH1/crozotinib (cancer) - 4c9w

8. Jeremy Gilbride, Ross Furash, Michael Grunwald, Lauren Okamoto, Laura Ornes, Randy Phan Sulfonylpiperidines/Thymidylate Kinase Inhibitor - Antibacterial | 4hld

9. Elvan Cavac, Nerses Haroutunian, Nick Hoffman-Klaucke, Sarah Johnson, Christina Lincoln, Bach Pham, Zachary Plourde : GSK-3 beta complexes with inhibitors 1q3d

10. Brian Cain, James Conner, William Doherty, Kyle Missaggia, Anya Novikova, Soo Lim Eunice Park: Estrogen receptor beta/genistein complex - 1x7j

ExamplesExamples

See 2012 Team Projects

HelpHelp

Questions & AnswersQuestions & Answers

Here is a place to post questions and answers for each other about how to do things in Proteopedia. Here are some from me and previous students.

• For step-by-step instructions on creating example scenes, try Proteopedia:DIY:Scenes.

• A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).

• To show the biological unit, follow directions at Biological Unit: Showing. The pdb file will display the "asymmetric unit" = the smallest unit that can be replicated to generate the full crystal. Example: the protein may function as a dimer (you need biochemical experiments to tell you this -- crystallography and NMR won't tell you), but the pdb file may display a monomer (if the dimer is symmetric) or two dimers (if they have slightly different conformations in the crystals -- perhaps due to crystal contacts or perhaps representing 2 functional states of the protein!).

• Instructions for references are at Help:Editing#Citing_Literature_References.You can follow the format used in the example on the Asp receptor and they will be put in automatically.

You just find out the PMID code (listed in pubmed for example) and insert it into the following, at the place where you want the reference cited (click edit to see what is actually inserted here). You also need to add the section:

References

• Hey guys this is just a useful tip:

If you get an xml error after you try to save your changes it is due to the green scene coding. Our group experienced this issue and it would not let us access our sandbox. In order to fix this go back (or find the page to edit in your history) and delete the green scene code that was just entered. Then save the page and you should be back to your sandbox. This may be trivial to many, but just throwing it out there.

• To highlight some interesting portion of your protein:

Under the selections tab, you can "limit to residue numbers." So for example enter in 60-65, then click "replace selection" below. Then if you go to the colors tab you can pick a color for just the residues you have selected. If it is a loop or if they are hard to see you can go to the representation tab and set selection to ball and stick or spacefill.

It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.

• If you suddenly can't get to your sandbox page (error message XML error: Mismatched tag at line 1), try Help:Errors

Tips from feedback/edits of past year Proteopedia ProjectsTips from feedback/edits of past year Proteopedia Projects

Each section should start with the line that inserts the Jmol window: then each scene for that section will appear in that window, along side your text (<300 words).

Every jmol window should have a caption so we know what we are looking at (include the name of the molecule and pdb code) Replace 'insert caption here' with 'your caption'.

Careful with repetition of the same points in multiple sections -- instead organize the topics logically and you can have multiple people contribute to a section if you want.

Feel free to work together on sections and add people to the credits if that helps to make a coherent and organized story.

Follow the correct format for references, including citations in text -- see instructions and link above.

Make green scenes to illustrate your points, and weave your scenes into the text.

Use colored text to help the reader easily see your points in the scene and to keep your text concise. For example "This view shows the 2 alpha helices packed against the 4-stranded antiparallel beta sheet." The word view would link to a scene in which the alpha helices are red and the beta sheet is blue. Go into edit mode on this page to copy the colored text section for use on your page. See also Help:Color_Keys.

Avoid a list of miscellaneous facts. Choose the most interesting points to tell us in some detail and illustrate with green scenes.

Tell your story with green scenes and minimal text!