First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
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 2013: CBI Molecules are due 12/4/13 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2013" or "Revised 2013". 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).
** Designates CBI Molecules Featured on CBI website
- 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
- New Fall 2013!! Molecular Playground/ClyA, Bib Yang
- Updated Fall 2013!! Molecular Playground/OmpG, Christina Chisholm
New Fall 2013! : **Molecular Playground/Homo-dimeric RcdA, Kamal K. Joshi
- **Molecular Playground/Hexameric ClpX, Joanne Lau
- Best CBI Molecule 2011
- 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
- New Fall 2013!! Molecular Playground/Executioner Caspase-7, Derek MacPherson, Maureen E. Hill
- [[Molecular Playground/Caspase-3 Regulatory Mechanisms, Scott Eron, Bay Serrano, Yunlong Zhao
- 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
- New Fall 2013!! Molecular_Playground/Hsp70-Hsp90, Jill Graham
- New Fall 2012!! Molecular_Playground/ERDj5, Lydia Lamriben
- Molecular Playground/Saposin C, Abla Tannous
- Molecular_Playground/ERMan1, Johan Sunryd
- Updated Fall 2012!! Molecular_Playground/Pcr H, Fabian Romano, Carolina Morell-Pérez
- New Fall 2012!! Molecular Playground/Protective Antigen, Jing Huang
- New 2013! Molecular Playground/Inteferon, Chengfeng Ren
- Updated Fall 2012!! Molecular Playground/Transferrin, Khaja Muneeruddin, Jake Pawlowski
- Molecular Playground/Velaglucerase, Adriana Kita
- New Summer 2014!! Molecular Playground/Antithrombin-Heparin, Yunlong Zhao
- Updated Fall 2013!! Molecular Playground/FIH, Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky
- Updated Fall 2012!! Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin, Serap Pektas
- Best CBI Molecule Proteopedia Page 2010
- Molecular Playground/Nickel Superoxide Dismutase, Carolyn Carr
- Updated Fall 2013!! Molecular Playground/CsoR and RcnR, Heidi Hu, Carolyn Carr
- Molecular Playground/HypA, 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
- New Fall 2013! Molecular Playground/MMP14, Lauren Jansen
- 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
- New Fall 2013! Molecular Playground/Streptavidin, Katrina Rieger
- New Fall 2012!! Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp), Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey
- Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey
- Molecular Playground/ACP apo, Gitanjeli Prasad
- New Fall 2012!! Molecular Playground/Tic40, Mine Canakci
- Updated Fall 2013!! Molecular Playground/HIV Tat, Brittany deRonde
- New Fall 2013!! Interleukin-1 beta, Huan He
- 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
- New Fall 2013!! Molecular Playground/Bacterial Chemotaxis Complex, Elizabeth R. Haglin, Maryam Kashefi
- New Fall 2012!! Molecular Playground/CheA, Elizabeth R. Haglin
- Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones
- Updated 2013!! Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima, Xuni Li
- New Fall 2013!! Molecular Playground/Human Serum Albumin, Mahalia Serrano
- 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/β-lactoglobulin, Daniel Seeman, Dubin Lab
- Molecular Playground/ADAM13, Genevieve Abbruzzese, Alfandari Lab
The 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 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321.
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.
1. If you don't already have one, request a Proteopedia account and log in.
2. Read through the rest of the instructions and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop.
3. 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).
4. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the 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.
5. 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, and then "new 2013" or "revised 2013".
Links 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.
Proteopedia Page Contributors and Editors (what is this?)
Lynmarie K Thompson, Carrie Morrison Penland, Khaja Muneeruddin, Yuping Zhou, Daniel Seeman, Eric Martz, Brittany deRonde, Luis E Ramirez-Tapia, Lawrence Sheringham Borketey, Gitanjeli Prasad, Heidi Hu, Derek MacPherson, Carolyn Carr, Yadilette Rivera-Colon, Tsung-Yi Lin, Lauren Jansen, Chengfeng Ren, Kamal K. Joshi, Kevin Buadlart Dagbay, Miaomin Zhang, Whitney Stoppel, Nick Borotto, Yunlong Zhao, Bib Yang, Xuni Li, Huan He, Joanne Lau, Katrina Rieger, Elizabeth R. Haglin, Rui Tang, Carolina Morell-Perez, Nilima Kolli, Jing Liu, Daniel Moyano-Marino, Thuy V. Nguyen, Joe White, Abla Tannous, Ankit Vahia, Shaynah Browne, Mahalia Serrano, Mine Canakci, Banyuhay P. Serrano, Lydia Lamriben, Shiela M. Jones, Rohan Patil, Judy Ventura, Adriana Kita, Reuben Chacko, Gustavo Elberto Epalza Sanchez, David Griffin, Ketan Mathavan, Daniella C. Gonzalez-Toro, Kristine Faye Pobre, Mariel Feliciano, Dannielle Ryman, Diego Amado-Torres, Jaime Prilusky, Maryam Kashefy, Erika M. Saffer, Vanessa Chaplin, Karan Hingorani, Genevieve Abbruzzese, Jiaming Zhuang, Krishna Reddy Ragupathi, Sarah Wilson, Zhe Zhang, Jan Panteli, Jing Huang, Christina Chisholm, Jake Pawlowski, Kristen Huber, Serap Pektas, Meili Yang, Muslum Yildiz, David Solfiell, Mangai Periasamy, Johan Sunryd, Cristina B. Martin, Bradley Duncan, Samantha B. Nicholls, Charles Swofford, Jing Guo, Gladys Wanjiku Murage, Rami Rajasekhar Reddy, John Hangasky, Ralph A. Francescone III