Student Projects for UMass Chemistry 423 Spring 2016: Difference between revisions

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:3. '''Start your team’s sandbox page by completing the "See Also" section by Monday 2/8. Are any human-authored Proteopedia pages too similar?'''
:3. '''Start your team’s sandbox page by completing the "See Also" section by Monday 2/8. Are any human-authored Proteopedia pages too similar?'''
Enter or edit your team's topic name and pdb code, and byline names. Complete the "See Also" section: add links to any related Proteopedia Topic Pages (not pages titled with the pdb code). Search for these, for example at http://proteopedia.org/wiki/index.php/Category:Topic_Page, Topic_pages, and Proteopedia:structure_Index. If you find another useful search strategy, post it under Help at Sandbox 423. If there is another page describing a complex with the same or a very similar molecule, you will need to choose a new topic.
Enter or edit your team's topic name and pdb code, and byline names. Complete the "See Also" section: add links to any related Proteopedia Topic Pages (not pages titled with the pdb code). Search for these, for example at http://proteopedia.org/wiki/index.php/Category:Topic_Page, Topic_pages, and Proteopedia:structure_Index. If you find another useful search strategy, post it under Help at Sandbox 423. If there is another page describing a complex with the same or a very similar molecule, you will need to choose a new topic.
:4. '''Sandbox page displaying initial structure and one green scene due by end of class workshop 2/10 -- bring your computers to class.'''
:4. '''Sandbox page displaying initial structure and one green scene due by end of class workshop 2/12 -- bring your computers to class.'''
In your assigned sandbox page click "edit this page" (top) and follow the directions to insert your rotating structure on your page. Describe and illustrate with a green scene the secondary structure of your protein.
In your assigned sandbox page click "edit this page" (top) and follow the directions to insert your rotating structure on your page. Describe and illustrate with a green scene the secondary structure of your protein.
:5. '''Sandbox page with each section displaying an outline and at least one green scene due by beginning of class 2/22 -- bring your computers to class.'''
:5. '''Sandbox page with each section displaying an outline and at least one green scene due by beginning of class 2/24 -- bring your computers to class.'''
Each team member should read the primary reference for the pdb structure and create an outline for their section and at least one green scene. Teams will meet briefly during class to discuss the overall organization as needed to make it logical and avoid duplication. As individuals proceed to create their sections, they should watch the other sections and stay in contact as needed to create a coherent overall project.
Each team member should read the primary reference for the pdb structure and create an outline for their section and at least one green scene. Teams will meet briefly during class to discuss the overall organization as needed to make it logical and avoid duplication. As individuals proceed to create their sections, they should watch the other sections and stay in contact as needed to create a coherent overall project.
:6. '''Project completed (all sections) in Proteopedia by Sun 4/10. All team members also submit their text to Turn It In (see class Moodle page).'''
:6. '''Project completed (all sections) in Proteopedia by Sun 4/10. All team members also submit their text to Turn It In (see class Moodle page).'''
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===Project Description===
===Project Description===
''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-e of the team project.''
''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-e of the team project.''
Each section should have its own JMol window. Provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Be concise (<300 words)! Do not include any copyrighted figures! All sections must be written in your own words with citations to your sources, following the reference format in the example below (go into edit this page, to see how these references were done). You may include links to other interesting information or scenes but you must create your own scenes for display on your page.  
All sections will be within a single scrolling section (single JSmol window) -- I changed to this in March to speed up loading. Provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Be concise (<300 words)! Do not include any copyrighted figures! All sections must be written in your own words with citations to your sources, following the reference format in the example below (go into edit this page, to see how these references were done). You may include links to other interesting information or scenes but you must create your own scenes for display on your page.  


''Make it interesting and accessible to a non-scientist!  Show clearly some chemical details to illustrate the chemistry of life processes!''
''Make it interesting and accessible to a non-scientist!  Show clearly some chemical details to illustrate the chemistry of life processes!''
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:For the 2/8 deadline, all team members should look for related Proteopedia pages (e.g. same protein but with different ligands) and post links here.
:For the 2/8 deadline, all team members should look for related Proteopedia pages (e.g. same protein but with different ligands) and post links here.


g. Credits -- list who did which portion of the project. Teams with 6 members should have the additional person write an additional quiz question.
g. Credits -- list who did which portion of the project. If multiple people work on a section, use an asterisk to designate one person with primary responsibility.
:Introduction -- name of team member
:Introduction -- name of team member
:Overall structure -- name of team member
:Overall structure -- name of team member
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==Help==
==Help==


===Questions & Answers===
===Tips, Questions, & Answers===


Here are some questions/answers from me and previous students. Post new ones at [[Sandbox423]], where you can also find links to past projects.
Here are some tips/questions/answers from me and previous students. Post new ones at [[Sandbox423]], where you can also find links to past projects.


*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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==Teams, Topics, and Links 2016==
==Teams, Topics, and Links 2016==


'''Team 1:''' Julie Boshar,
'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar,
Emily Boyle,
Emily Boyle,
Nicole Kirby,
Nicole Kirby,
Cory Thomas,
Cory Thomas,
Connor Walsh
Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)


'''Team 2:''' Michael Beauregard,
'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
Annie Burton,
Annie Burton,
Jianlong Li,
Jianlong Li,
Daniel Marco,
Daniel Marco,
Nathaneal Park
Nathaniel Park -- Drug intercalation complex of DNA (1xcs)
 
'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
Robert Green,
Uday Prakhya,
Nicholas Rivelli,
Elizabeth Swanson -- Vitamin D binding protein (1j7e)
 
'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
Kate Daborowski,
Patrick Murphy,
Benjamin Rizkin,
Aaron Thole -- Vitamin D receptor/vitamin D (1db1)
 
'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
Samuel Pierce,
Hyunjoon Choi,
Anton El Khoury,
Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor)  (2jch)
 
'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
Lauren Timmins,
Aidan Finnerty,
Adam Murphy,
Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)
 
'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
Elizabeth Humble,
Kati Johnson,
Samantha Kriksceonaitis,
Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)
 
'''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley,
Katie Kwan,
Daniel Peters,
Ishtiaque Rafiyu,
Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)
 
'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park,
Marissa Burgess,
Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)
 
'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler,
Patrick Tonne,
Owen O'Connor,
Tyler Russell,
Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)
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