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'''This sandbox is in use until August 1, 2011 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!'''


==''' Spring 2016 Chem423 Team Projects'''==
'''Understanding the chemical basis of disease and life processes'''


'''Team & Structure selection, due 3/30/11'''
Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]].
:Form teams of 4 people; include both chemistry and chemical engineering majors on each team. Start by finding a protein-drug or nucleic acid-drug complex with a known structure that interests your team (see assignment sheet instructions). Check the list below to see if another team has already chosen this complex.  If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model).


:Copy the message at the top of this page into your sandbox page to "reserve" this sandbox for this course.
''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.''


:Find the pdb id for your protein-drug complex in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page. You can use the edit button on any page to find out how other users created effects that you see.
'''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.'''


:Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar,
and display another structure.
Emily Boyle,
Nicole Kirby,
Cory Thomas,
Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)  


'''Project completion, due 4/22/11'''
'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
''Your proteopedia page should be organized into the following 4 required sections, with each team member responsible for one of these sections of the team project.''
Annie Burton,
Jianlong Li,
Daniel Marco,
Nathaniel Park -- Drug intercalation complex of DNA (1xcs)


1. Introduction
'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
:Introduce the protein function and the disease treated by the drug. This must be written in your own words with citations to your sources.You cannot include a copyrighted figure unless you request information to use it.
Robert Green,
2. Overall structure
Uday Prakhya,
:Describe the overall structure of your protein in words and make "green scenes" to illustrate your points. What elements of secondary structure are present (ie 5 alpha helices and 2 beta strands) and how are they organized? Below I illustrate the start of an "overall structure" section on GFP. Additional description and green scenes could illustrate the polar/nonpolar distrubution of amino acids (is the inside of the barrel polar or nonpolar?), packing of amphipathic elements, etc.
Nicholas Rivelli,
3. Drug binding site
Elizabeth Swanson -- Vitamin D binding protein (1j7e)
:Describe features of the drug binding site in words and make "green scenes" to illustrate your points. What interactions stabilize binding of this molecule to the protein.
4. Additional features
:Describe and use green scenes to illustrate additional features of the protein. What you do here depends on what information is available. If a structure of the protein-substrate complex is available, you could compare protein interactions with the substrate vs. with the drug. If the drug is a transition state inhibitor, explain and illustrate that (include figures describing the reaction).


Credits -- at the end list who did which portion of the project:
'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
:1. Introduction -- name of team member
Kate Daborowski,
:2. Overall structure -- name of team member
Patrick Murphy,
:3. Drug binding site -- name of team member
Benjamin Rizkin,
:4. Additional features -- name of team member
Aaron Thole -- Vitamin D receptor/vitamin D (1db1)


== Overall Structure ==
'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
Samuel Pierce,
Hyunjoon Choi,
Anton El Khoury,
Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor)  (2jch)


{{STRUCTURE_1ema | PDB=1ema  |  SCENE=  }}
'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
The <scene name='Sandbox3/Secondary_structure/1'>overall structure</scene>  of green fluorescent protein is an 11-stranded antiparallel beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from [[1ema]].
Lauren Timmins,
Aidan Finnerty,
Adam Murphy,
Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)


==='''Chem423 Sandbox pages:'''Student projects:===
'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
Elizabeth Humble,
Kati Johnson,
Samantha Kriksceonaitis,
Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)


Jamal Salah & Vishwa Shah- deoxyhemoglobin ([[sandbox4]])
'''[[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,
Daniel Estabrook,
Marissa Burgess,
Miranda Goldman,
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)
 
== Examples ==
See
 
[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
 
[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
 
[[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]]
 
==Help==
See  [[Student Projects for UMass Chemistry 423 Spring 2016|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

Latest revision as of 17:48, 3 March 2016

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

Spring 2016 Chem423 Team ProjectsSpring 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)

ExamplesExamples

See

2015 Team Projects

2012 Team Projects

2011 Team Projects

HelpHelp

See Help

Questions & AnswersQuestions & 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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Lynmarie K Thompson, Student, Joe Perito, Louis Pires, Arash Manafirad
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