CBI Molecules: Difference between revisions
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:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin | :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas | ||
:: Best CBI Molecule Proteopedia Page 2010 | :: Best CBI Molecule Proteopedia Page 2010 | ||
Revision as of 23:50, 12 December 2012
These are molecules under study by members of the University of Massachusetts Amherst Chemistry-Biology Interface Program. Many of the molecules we study are featured at the Molecular Playground (see also Molecular Playground in Proteopedia). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.
UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.
Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).
MoleculesMolecules
** Designates CBI Molecules Featured on CBI website
Bhatia Lab
- Molecular Playground/Alginate-Fall2011, Joe White, David Griffin
- Molecular Playground/Alginate-Fall2010, Joe White, David Griffin
- Molecular Playground/Poly(ethylene glycol), Erika M. Saffer
- Molecular Playground/Glutamate Receptor, Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano
- **Molecular Playground/Hexameric ClpX, Joanne Lau
- Best CBI Molecule 2011
Forbes Lab
- Molecular Playground/CheR, Miaomin Zhang
- Molecular Playground/RBP, Jan Panteli
- Molecular Playground/TRAIL, Charley Swofford
- Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon
- Molecular Playground/Human PPCA, Nilima Kolli
- Molecular Playground/CRABP I, Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy
- Best Overall CBI Molecule 2010
- Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein), Gustavo Elberto Epalza Sanchez
(compare this to the previous version above to see what's new)
- **Molecular_Playground/DHFR, Karan Hingorani
- Best CBI Molecule 2012
- Molecular Playground/Caspase-6 and neurodegeneration, Kevin Buadlart Dagbay
- Molecular Playground/Caspase-9 Regulation, Kristen Huber
- Molecular Playground/Caspase-6 (new), Elih Velazquez
- Molecular Playground/Influenza A M2 transmembrane domain, Samantha Nicholls
- Molecular Playground/Dengue Virus Protease, Muslum Yildiz
Hebert Lab
- Molecular Playground/Saposin C, Abla Tannous
- Molecular_Playground/ERMan1, Johan Sunryd
- Molecular_Playground/Pcr H, Fabian Romano
- Molecular Playground/Transferrin, Khaja Muneeruddin
- Molecular Playground/Velaglucerase, Adriana Kita
Knapp lab
- Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin, Serap Pektas
- Best CBI Molecule Proteopedia Page 2010
- Molecular Playground/FIH, Cornelius Taabazuing, Breanne Holmes, John Hangasky
- Molecular Playground/Nickel Superoxide Dismutase, Carolyn Carr
- Molecular Playground/CsoR and RcnR, Heidi Hu
- **Molecular Playground/T7 RNAP Conformations, Luis E. Ramirez-Tapia
- Best CBI Molecule 2011
- Molecular Playground/T7 RNA Polymerase (7 mer int), Ankit Vahia
- Molecular Playground/Human mtRNA pol, Ketan Mathavan
Peyton Lab
- Molecular Playground/C-Raf, Thuy Nguyen
- Molecular Playground/FAK, Dannielle Ryman
- Molecular Playground/Taxol, Rohan Patil, Sarah Wilson
- Molecular Playground/Insulin, Whitney Stoppel
- Molecular Playground/Reverse Transcriptase, Daniel Moyano-Marino
- Molecular Playground/Pancreatic Lipase, Rui Tang
- Molecular Playground/Targeting Peptide, David Solfiell
Schnarr Lab
- Molecular Playground/Sfp, Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey
- Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso
- Molecular Playground/ACP apo, Gitanjeli Prasad
Tew Lab
- Molecular Playground/HIV Tat, Brittany deRonde
Thayumanavan Lab
- Molecular Playground/Lysozyme , Daniella Gonzalez
- Molecular Playground/Beta-galactosidase, Judy Ventura
- Molecular Playground/Carbonic Anhydrase, Krishna Reddy Raghupathi
- Molecular Playground/Avidin, Rami Rajasekar Reddy
- Molecular Playground/Biotin binding avidin, Diego Amado
- Molecular Playground/MMP12, Jiaming Zhuang
- Molecular Playground/Gluconase, Jing Guo
- Molecular Playground/Glutathione Reductase, Reuben Chacko
Thayumanavan & Vachet Labs
- Molecular Playground/Trypsin, Gladys Murage
- Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones
- Molecular playground/beta 2 microglobulin, Nick Borotto
- Best CBI Molecule Jmol scenes 2010
- Molecular Playground/Myoglobin, Yuping Zhou
- Molecular Playground/ Copper-Zinc Superoxide Dismutase, Shaynah Browne
Other Molecules of interest
- Molecular Playground/PcrA Helicase, Luis E Ramirez-Tapia, Martin Lab
Other Laboratories
- Molecular Playground/YKL-40, Ralph A. Francescone III, Shao Lab
- Molecular Playground/β-lactoglobulin, Daniel Seeman, Dubin Lab
- Molecular Playground/ADAM13, Genevieve Abbruzzese, Alfandari Lab
InstructionsInstructions
Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.
Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.
1. If you don't already have one, request a Proteopedia account and log in.
2. Get started working in Proteopedia by using the links at Help:Contents. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).
3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.
You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.
A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.
4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.
Links to HELP pagesLinks to HELP pages
Overview at Help:Contents
See also Help:Getting_Started_in_Proteopedia
Videos showing how to use Proteopedia: Proteopedia:Video_Guide (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)
Proteopedia Scenes: Do It Yourself gives succinct step by step instructions on how to create a molecular scene.
A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link. Proteopedia Workshop Slides
Proteopedia:Guidelines for Ethical Writing. Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.
For other help resources, click on Help in the navigation box at the upper left of every page in Proteopedia.