Sandbox423

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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!'''
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'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''
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'''Chem423 Team Projects: Understanding Drug Mechanisms'''
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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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== Project Instructions ==
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]].
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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. Team & Structure selection, due 4/1/11: All projects & names must be posted on the list below, linking to sandbox pages displaying initial structure.'''
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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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: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 in the pdb that interests your team. 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).
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:Copy the message at the top of this page into your sandbox page to "reserve" your sandbox for this course.
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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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:Find the pdb id for your protein-drug complex in the Protein Data Bank. In your sandbox page click"edit this page" (top) and follow the directions to insert your rotating structure on your page.
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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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'''2. Project completion, due 4/22/11'''
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'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
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''Your proteopedia page should be organized into the following 5 required sections, with each team member responsible for one of these sections of the team project.''
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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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a. Introduction
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'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
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: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 permission to use it.
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Kate Daborowski,
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b. Overall structure
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Patrick Murphy,
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: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.
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Benjamin Rizkin,
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c. Drug binding site
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Aaron Thole -- Vitamin D receptor/vitamin D (1db1)
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:Describe features of the drug binding site in words and make "green scenes" to illustrate your points. Show the interactions that stabilize binding of this molecule to the protein (ie H bonds).
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d. Additional features
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: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 (eg include a reaction scheme with structures of the substrate, transition state and product).
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e. Credits -- at the end list who did which portion of the project:
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'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
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:Introduction -- name of team member
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Samuel Pierce,
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:Overall structure -- name of team member
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Hyunjoon Choi,
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:Drug binding site -- name of team member
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Anton El Khoury,
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:Additional features -- name of team member
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Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch)
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f. References
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'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
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This will include the published paper that describes your structure (the reference associated with your pdb code). You will get much of your information about specific interactions to look for and highlight in the structure from this reference (which is much easier than trying to find these on your own with no guidance!).
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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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'''3. In-class presentations, to be announced'''
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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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== Example ==
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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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This is a complex between a macromolecule and its ligand (but this ligand is not a drug) that illlustrates the use of green scenes:
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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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{{Clear}}
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'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler,
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<applet load='1wat' size='[450,338]' frame='true' align='right'
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Patrick Tonne,
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caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>
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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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== Examples ==
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See
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'''Asp Receptor Ligand-binding domain'''
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
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'''Overall structure'''
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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The ligand binding domain of the aspartate receptor (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is a dimer of two 4-helix bundles that is shown here with the <scene name='SandboxLKT/Asplabel/2'>aspartate ligand</scene> bound.<ref>PMID: 8486661</ref> In this <scene name='SandboxLKT/Totmhelices/2'>rainbow representation</scene> the <font color='blue'>N</font> and <font color='red'>C</font> termini are at the bottom of the structure; this is where the connections to the transmembrane helices have been truncated.
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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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==Help==
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See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
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'''Ligand binding site'''
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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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Interactions that stabilize ligand binding<ref>PMID: 1660187</ref> include hydrogen bonding from Tyr149 and Gln152 backbone carbonyls and Thr154 sidechain OH to the <scene name='SandboxLKT/Asp_ligand_aminohbonds/5'>ligand amino group</scene> and hydrogen bonding from the sidechain nitrogens of Arg64, Arg69, and Arg73 to the two <scene name='SandboxLKT/Asp_ligand_carboxylhbonds/4'>ligand carboxyl groups</scene>.
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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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<scene name='Sandbox423/Hbond/1'>test</scene>
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Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest
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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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'''References'''
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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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<references/>
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== Project Teams, Topics, and Links ==
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4/6/11 '''Feedback''' from LKT here or on your pages -- please remove or respond to my comment when you've addressed it.
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'''G''' Great start.
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'''S''' Needs structure of your complex, replacing generic structure.
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'''PS''' Needs linked page with structure of your complex.
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'''C''' See comment on your page.
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Example (but not a drug complex): Lynmarie Thompson, ..., ..., ... - Asp receptor in complex with Asp (above)
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'''S''' Nick DeGraan-Weber, Jackie Dorhout, Rachael Jayne, Mike Reardon - flu neuraminidase in complex with tamiflu [[sandbox45]]
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'''G''' Varun Chalupadi, Anthony Laviola, Tiffany Brucker, Alan Stebbins - cyclooxygenase [[sandbox25]]
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'''G''' Brittany Forkus, Katie Geldart, Elizabeth Schutsky, Breanna Zerfas - beta adrenergic GPCR [[sandbox226]]
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'''PS''' Max Moulton, Sally Stras, Jordan Schleeweis, Anh Huynh -- HIV reverse transcription [[Sandbox77]]
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'''S''' Lucia Tringali, Shaina Boyle, Jaclyn Somadelis , Dany Mbakop -- HIV Protease [[Sandbox17]]
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'''G''' Chris Brueckner, Daniel Roy, John Clarkson, Justin Srodulski -- Ketamine in binding complex with NMDA receptor [[sandbox42]]
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'''C''' Andy Kim, Zach Brentzel, Tyler Vlass, Zach Hitzig -- Acetylcholinesterase [[sandbox11]]
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'''G''' Inna Brockman, Robert Nathan, Sarena Horava, Nick Cadirov - p38 kinase [[sandbox713]]
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'''C''' John Hickey, Josh Drolet, Josephine Harrington, Andrea Simoni - influenza M2 proton channel [[sandbox 111]]
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'''G''' David Peltier, Donald Einck, Ethan Leighton, Chris Coakley - Rituximab Fab [[sandbox99]]
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'''PS''' Lyes Khendek, Paul Breslin, William Rowley - G-Quadruplex [[sandbox888]]
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==Students looking for group members==
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Each group should contain at least one person from a different primary major (typically Chemistry or Chemical Engineering) than the rest.
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List yourself + your major, list partial groups looking for members, list your complex if you have chosen one. Contact others to form a group.
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4/1/11 update by Prof Thompson: The remaining students can go ahead and form teams regardless of major.
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Luis Cristian, Chem major, lcristia@student.umass.edu - looking to be in a group with chem eng
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Joe Perito, Chem major, jperito@student.umass.edu - looking for a group
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==Help Editing==
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Hint: Ctl-click or right-click on links below and select "Open Link in New Window"
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Start with Help in the navigation box on the left. Some things I've found useful:
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*Follow the step-by-step written [[Proteopedia:Primer|Primer]].
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*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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*For editing help, try [[Help:Editing]]. Guidelines for avoiding plagiarism are listed here: [[Proteopedia:Guidelines for Ethical Writing]].
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*You can use the edit button on any page to find out how other users created effects that you see in the text (not the scenes).
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[[http://meta.wikimedia.org/wiki/Cheatsheet Wikimedia cheat sheet]]
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[[http://en.wikipedia.org/wiki/How_to_edit General help with Wiki editing]], plus more [[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Text examples]]
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Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.
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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:
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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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