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: Understanding the chemical basis of disease and life processes'''==
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==''' Spring 2016 Chem423 Team Projects'''==
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'''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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1. Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett - [[Sandbox Reserved 425|Catechol-O-methyltransferase, 2ZVJ, Parkinson's disease]]
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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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2. William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen - [[Sandbox Reserved 426|Hemoglobin 1qxd ]]
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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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3. Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop - [[Sandbox Reserved 427|Diabetes 2DTG (insulin receptor) ]] also consider 3loh
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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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4. Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet - [[Sandbox Reserved 428|1rva]]
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'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
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Robert Green,
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5. Alex Gramann, William Frantz, Felix Alfonso, Paula Preap - [[Sandbox Reserved 429| Bone Formation & Apoptosis & 1m4u ]]
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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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6. Greg Keohane, Nicole Hofstetter, Gina Lein, Louis Pires, - [[Sandbox Reserved 430|cisplatin, 1a84 ]]
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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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7. Polina Berdnikova, James Hamblin, Jill Carlson, Brett Clinton - [[Sandbox Reserved 431|phosphatase inhibitor complexes-1nny]]
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'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
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Samuel Pierce,
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8. Max Nowark, Kyle Reed, Kevin Dillon, Chris Carr - [[Sandbox Reserved 432|dementia 1JVQ ]]
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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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9. Di Lin, Jill Moore, Austin Virtue, Alexander Way - [[Sandbox Reserved 433|Caspase 3, 1RHK ]]
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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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10. Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley - [[Sandbox Reserved 434|leadzyme, 1nuv]]
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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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Xuni Li - [[Sandbox Reserved 435|examples]]
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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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More possible topics
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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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restriction enzyme complexes: 1rva, 1rvb, 1rvc
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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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==Questions & Answers==
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== Examples ==
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See
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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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[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
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*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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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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[[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]]
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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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==Help==
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See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
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*Anyone know what format we should be putting our references in?
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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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For references, follow the format used in the example on the Asp receptor and they will be put in automatically.
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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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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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Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest
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<references/>
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*Hey guys this is just a useful tip:
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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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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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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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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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For example:
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selections: DNA, replace selection
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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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selections: invert selection (back to DNA)
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representations: backbone, set representation

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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