Sandbox423

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'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''
'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''
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==''' Spring 2012 Chem423 Team Projects'''==
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==''' Spring 2016 Chem423 Team Projects'''==
'''Understanding the chemical basis of disease and life processes'''
'''Understanding the chemical basis of disease and life processes'''
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2012]].
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]].
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==='''Presentation Dates, Teams, Topics, and Links'''===
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''Each team should together agree upon a topic and pdb code (check the list below to be sure your topic is not already taken), then log in to Proteopedia (see instructions in Moodle) and edit this section to list your topic and pdb code.''
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Following any team's entry, add your nominations of the best scenes for display at the ISB Molecular playground, using the following format:
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"Your Name" nominates the scene "name of green scene" with the caption "your caption".
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'''2/8/16 Topics are all set and copied to [[Student Projects for UMass Chemistry 423 Spring 2016]] -- notify Prof Thompson of any changes by email.'''
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Choose a visually attractive scene and come up with a new caption of ≤ 12 words that is interesting/understandable to a general audience. See my example under the first project. Be creative!
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3. Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop - [[Sandbox Reserved 427|Diabetes 3loh (insulin receptor) ]] '''Presentation 3/28/12''' '''Draft due 3/21'''
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'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar,
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Emily Boyle,
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Nicole Kirby,
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Cory Thomas,
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Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)
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Prof Thompson nominates the scene "biological dimer" with the caption "Insulin receptor signaling goes awry in diabetes".
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'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
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Annie Burton,
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Jianlong Li,
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Daniel Marco,
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Nathaniel Park -- Drug intercalation complex of DNA (1xcs)
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Rebecca Bishop nominates the scene "biological dimer" with the caption "Understanding insulin receptor signaling may be the key to treating Type II Diabetes."
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'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
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Robert Green,
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Uday Prakhya,
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Nicholas Rivelli,
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Elizabeth Swanson -- Vitamin D binding protein (1j7e)
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Stephanie Bristol nominates the scene "hexamer form" with the caption "The hexamer form of insulin that aids in storage in the pancreas but does not activate the insulin receptor."
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'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
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Kate Daborowski,
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Patrick Murphy,
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Benjamin Rizkin,
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Aaron Thole -- Vitamin D receptor/vitamin D (1db1)
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6. Greg Keohane, Nicole Hofstetter, Gina Lein, Louis Pires, - [[Sandbox Reserved 430|cisplatin, 1a84 ]] '''Presentation 4/9/12''' '''Draft due 4/2'''
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'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
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Samuel Pierce,
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Hyunjoon Choi,
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Anton El Khoury,
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Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch)
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Jeffrey Boerth nominates the scene "binding interactions" with the caption "Cisplatin binding to adjacent guanine bases halts tumor cell growth in cancer therapy."
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'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
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Lauren Timmins,
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Aidan Finnerty,
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Adam Murphy,
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Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)
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Louis Pires nominates the scene "DNA" with the caption "Cisplatin binding bends DNA creating a new direction in cancer research."
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'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
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Elizabeth Humble,
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Kati Johnson,
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Samantha Kriksceonaitis,
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Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)
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Gina Lein nominates the scene “DNA” with the caption “HMG-Protein kinks DNA further leading to tumor cell death.“
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'''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley,
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Katie Kwan,
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Daniel Peters,
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Ishtiaque Rafiyu,
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Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)
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"Nicole Bundy" nominates the scene "A-DNA conformation due to Cisplatin" with the caption "Cisplatin is leaps and "bends" above the rest; bending DNA strands to fight cancer!".
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'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park,
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Daniel Estabrook,
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Marissa Burgess,
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Miranda Goldman,
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Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)
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Chris Carr nominates the scene "DNA" with the caption "HMG-Protein: binding and disrupting cancer cell DNA".
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'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler,
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Patrick Tonne,
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Owen O'Connor,
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Tyler Russell,
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Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)
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4. Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet - [[Sandbox Reserved 428|restriction enzyme/DNA complex, 1rva ]] '''Presentation 4/11/12''' '''Draft due 4/4'''
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== Examples ==
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See
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Felix Alfonso nominates the scene "specific" with the caption "Target site recognition along the DNA Minor Groove by EcoRV endonuclease restriction enzyme"
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
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Emily Brackett nominates the scene "recognition sequence" with the caption "EcoRV endonuclease bound to DNA to cleave between the A and T base pairs".
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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5. Alec Gramann, William Frantz, Felix Alfonso, Paula Preap - [[Sandbox Reserved 429| Bone Formation & Apoptosis & 1m4u ]] '''Presentation 4/23/12''' '''Draft due 4/16'''
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Max Nowak nominates the scene "dimer" with the caption "Noggin-BMP-7 complex shows inhibition of chrondogenesis in chicks"
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]]
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9. Di Lin, Jill Moore, Austin Virtue, Alexander Way - [[Sandbox Reserved 433|Caspase 3, 1RHK ]] '''Presentation 4/23/12''' '''Draft due 4/16'''
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==Help==
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See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
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Julia Tomaszeski nominates the scene "DEVD-aldehyde binding" with the caption "My name is Bond - Hydrogen Bond."
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==Questions & Answers==
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Here is a place to post new questions and answers for each other about how to do things in Proteopedia. Good tips will be added to the Help section for future classes (above link).
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Austin Virtue nominates the scene "heterotetramer" with the caption "Alpha helixes surrounded twelve stranded beta sheet structure is unique to caspases"
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There is a recurring problem where sections below an edited section disappear (you can still see them in edit window). Don’t try to insert your scene into the command that loads the initial molecule (which may have caused the rest of the sections not to load). Write some text and then insert green scenes into text. -- Prof Thompson 2/17/16
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1. Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett - [[Sandbox Reserved 425|Catechol-O-methyltransferase, 2ZVJ, Parkinson's disease]] '''Presentation 4/25/12''' '''Draft due 4/18'''
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Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest
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Di Lin nominates the scene "aromatic ring" with the caption "These two aromatic rings were shown to be inhibitors in vitro and vivo of catechol-O-methyltnansfenase"
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1. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations.
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Greg Keohane nominates scene "aromatic ring" with the caption "shown to be inhibitors in vitro and in vivo of catechol-O-methyltnansfenase"
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2. Turn on selection halos (under the structure “show selected with halos” - click the ON button). They make it much easier to keep track of what is selected, especially after multiple "invert selection" commands.
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Nicole Hofstetter nominates scence "here" with caption "Multitasking enzyme Catechol-O-Methyltransferase , can extraordinarily be membrane bound or water soluble, a magnificent feature of its mixed polar and non-polar groups."
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For example:
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selections: DNA, replace selection
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Kyle Reed nominates the scene "here" (In Overall Structure) with the caption "Catechol-O-Methyltransferase and the polarity of its residues (purple=polar, gray=nonpolar)"
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invert current selection (selects all but DNA)
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representations: hide selection (hides all but DNA)
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8. Max Nowak, Kyle Reed, Kevin Dillon, Chris Carr - [[Sandbox Reserved 432|dementia 1JVQ ]] '''Presentation 4/25/12''' '''Draft due 4/18'''
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selections: invert selection (back to DNA)
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representations: backbone, set representation
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Nick Vecchiarello nominates scene "heterodimer" with the caption "heterodimer: Linkage of the L and I Chains"
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2. William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen - [[Sandbox Reserved 426|Hemoglobin 1qxd ]] '''Presentation 4/27/12''' '''Draft due 4/20'''
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William Frantz nominates the scene "α and β Subunits" with the caption "Four subunits intertwine and align to bind O2"
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Ryan Deeney nominates the scene "2Hbs Val6 interaction with hydrophobic patch" with the caption "Mutation in one amino acid causes a hydrophobic interaction, forming sickle cell hemoglobin"
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Jeffrey Salemi nominates the scene "Glu6 residue of Hb" with the caption "Sickle cell anemia stems from a single mutation in Glu6".
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Alec Gramann nominates the scene "αβ Dimers" with the caption "Sickle-cell anemia nickel and dimed the αβ Dimer, limiting oxygen binding."
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7. Polina Berdnikova, James Hamblin, Jill Carlson, Brett Clinton - [[Sandbox Reserved 431|phosphatase inhibitor complexes-1nny]] '''Presentation 4/27/12''' '''Draft due 4/20'''
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James Hamblin nominates the scene "three different stages" with the caption "Drug design: creating a ligand for increased insulin response"
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Tom Foley also nominates the scene "three different stages" with the verbose caption "This product of rational drug design blocks the active site and selectively binds localized non-active sites."
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Brett Clinton nominates the scene "three different stages" with the caption "A linked fragment inhibitor to treat diabetes."
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10. Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley - [[Sandbox Reserved 434|leadzyme, 1nuv]] '''Presentation 4/30/12''' '''Draft due 4/23'''
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William Yarr nominates the scene "here" with the caption "Leadzyme is an enzymatic, double-stranded RNA complex called a ribozyme."
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Kate Liedell nominates the scene "leadzyme" with the caption "Leadzyme: RNA can do more than information transfer in this RNA cutting ribozyme"
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===Questions & Answers===
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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.
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*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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*<font color='red'>Safari currently not working for making a scene...</font> LKT 2/27 But it just worked for Xuni! Test saving a simple scene first.
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*A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).
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*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!).
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*Anyone know what format we should be putting our references in?
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Complete 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.
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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).
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<ref>PMID: 8486661</ref>
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You also need to add the section:
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'''References'''
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<references/>
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*Hey guys this is just a useful tip:
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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.
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*To highlight some interesting portion of your protein:
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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.
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It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.
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*If you suddenly can't get to your sandbox page (error message XML error: Mismatched tag at line 1), try [[Help:Errors]]
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===Tips from feedback/edits of your Proteopedia Projects===
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Please read the feedback on all of the sections to give you ideas for improving your own section -- leave the red text until you're all done with all sections.
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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 (which should only extend 1-2 lines beyond the jmol window).
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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'.
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Captions in each section: come up with a cool (short) caption that fits your best scene that you think would be good for the Molecular Playground -- something that's understandable on its own and will capture the attention of a broad audience.
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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.
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Feel free to work together on sections and add people to the credits if that helps to make a coherent and organized story.
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Follow the correct format for references, including citations in text -- see instructions and link above.
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Make green scenes to illustrate your points, and weave your scenes into the text.
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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 <font color='red'>2 alpha helices </font> packed against the <font color='blue'> 4-stranded antiparallel beta sheet</font>." The word view would like 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.
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Avoid a list of miscellaneous facts. Choose the most interesting points to tell us in some detail and illustrate with green scenes.
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Keep the length of your text similar to the length of the jmol window.
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Current revision

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

Contents

Spring 2016 Chem423 Team Projects

Understanding the chemical basis of disease and life processes

Follow instructions posted at Student Projects for UMass Chemistry 423 Spring 2016.

Each team should together agree upon a topic and pdb code (check the list below to be sure your topic is not already taken), then log in to Proteopedia (see instructions in Moodle) and edit this section to list your topic and pdb code.

2/8/16 Topics are all set and copied to Student Projects for UMass Chemistry 423 Spring 2016 -- notify Prof Thompson of any changes by email.

Team 1: Julie Boshar, Emily Boyle, Nicole Kirby, Cory Thomas, Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)

Team 2: Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, Nathaniel Park -- Drug intercalation complex of DNA (1xcs)

Team 3: Alex Debreceni, Robert Green, Uday Prakhya, Nicholas Rivelli, Elizabeth Swanson -- Vitamin D binding protein (1j7e)

Team 4: Roger Crocker, Kate Daborowski, Patrick Murphy, Benjamin Rizkin, Aaron Thole -- Vitamin D receptor/vitamin D (1db1)

Team 5: Tyler Carpenter, Samuel Pierce, Hyunjoon Choi, Anton El Khoury, Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch)

Team 6: Cora Ricker, Lauren Timmins, Aidan Finnerty, Adam Murphy, Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)

Team 7: Isabel Hand, Elizabeth Humble, Kati Johnson, Samantha Kriksceonaitis, Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)

Team 8: Laura Feeley, Katie Kwan, Daniel Peters, Ishtiaque Rafiyu, Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)

Team 9: Soo Lim Park, Daniel Estabrook, Marissa Burgess, Miranda Goldman, Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)

Team 10: Luke Schnitzler, Patrick Tonne, Owen O'Connor, Tyler Russell, Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)

Examples

See

2015 Team Projects

2012 Team Projects

2011 Team Projects

Help

See Help

Questions & Answers

Here is a place to post new questions and answers for each other about how to do things in Proteopedia. Good tips will be added to the Help section for future classes (above link).

There is a recurring problem where sections below an edited section disappear (you can still see them in edit window). Don’t try to insert your scene into the command that loads the initial molecule (which may have caused the rest of the sections not to load). Write some text and then insert green scenes into text. -- Prof Thompson 2/17/16

Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest

1. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations.

2. Turn on selection halos (under the structure “show selected with halos” - click the ON button). They make it much easier to keep track of what is selected, especially after multiple "invert selection" commands.

For example: selections: DNA, replace selection invert current selection (selects all but DNA) representations: hide selection (hides all but DNA) selections: invert selection (back to DNA) representations: backbone, set representation

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