CBI Molecules
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.
It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.
Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries.
MoleculesMolecules
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/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
Kaltashov Lab
- Molecular Playground/Velaglucerase, Adriana Kita
Knapp lab
- Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin
- Best CBI Molecule Proteopedia Page 2010
- Molecular Playground/FIH, Cornelius Taabazuing, Breanne Holmes, John Hangasky
- Molecular Playground/T7 RNAP Conformations, Luis E. Ramirez-Tapia
- Best CBI Molecule 2011
- Molecular Playground/T7 RNA Polymerase (7 mer int), Ankit Vahia
- NEW Fall 2011! Molecular Playground/Human mtRNA pol, Ketan Mathavan
- 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/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso
- Molecular Playground/ACP apo, Gitanjeli Prasad
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! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!
Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.
Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.
1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.
2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example User:Lynmarie K Thompson/Sandbox 1).
3. Follow the format of the sample CBI molecule page Molecular Playground/Bacterial Chemotaxis Receptors. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.
4. Add a link to your sandbox page at Sandbox_CBI (CBI Molecules in Progress).
5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.
6. Choose a "green scene" on your Proteopedia page to suggest for display at the Molecular Playground and specify a "banner" which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."
7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.
8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.
Links to HELP pagesLinks to HELP pages
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.