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UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list. | UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list. | ||
Fall | Fall 2014: CBI Molecules are due 12/3/14 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 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not). | ||
Follow the instructions at the bottom of this page. | |||
==Molecules== | ==Molecules== | ||
'''** Designates CBI Molecules Featured on [ | '''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]''' | ||
[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab] | [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab] | ||
: | : '''[[Molecular Playground/ClyA]]''', Monifa Fahie, Bib Yang '''Revised 2014''' | ||
: | : '''[[Molecular Playground/OmpG]]''', Christina Chisholm, Monifa Fahie, Bib Yang '''Revised 2014''' | ||
[http://openwetware.org/wiki/Chien Chien Lab] | [http://openwetware.org/wiki/Chien Chien Lab] | ||
New | : '''[[Molecular Playground/ClpP]]''', Lisa Hernandez, Rob Vass '''New 2014''' | ||
: '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi | |||
: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau | : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011''' | ||
: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu | : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu | ||
Farkas Lab | Farkas Lab | ||
: '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014''' | |||
: '''[[Molecular Playground/ | |||
| Line 48: | Line 37: | ||
[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab] | [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab] | ||
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy | : '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014 | ||
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|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 | : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez | ||
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012''' | |||
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani | |||
[http://people.chem.umass.edu/jhardy/ Hardy Lab] | [http://people.chem.umass.edu/jhardy/ Hardy Lab] | ||
: | : '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill | ||
: '''[[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao | |||
: '''[[Molecular Playground/ | : '''[[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay | ||
: ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay | |||
: '''[[Molecular Playground/Caspase-7 Dynamics]]''' | : '''[[Molecular Playground/Caspase-7 Dynamics]]''' | ||
: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber | : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber | ||
: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez | : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez | ||
: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls | : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls | ||
: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz | : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz | ||
| Line 77: | Line 57: | ||
Hebert Lab | Hebert Lab | ||
: | : '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham "Revised 2014" | ||
: | : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben | ||
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous | : '''[[Molecular Playground/Saposin C]]''', Abla Tannous | ||
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd | : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd | ||
| Line 85: | Line 65: | ||
[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab] | [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab] | ||
: | : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang | ||
[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab] | [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab] | ||
: **'''[[Molecular Playground/Hemoglobin-Haptoglobin Complex]]''', Ololade Fatunmbi, Chibueze Egeruoh '''***New Fall 2014***''' | |||
: | : '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren | ||
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski | |||
: | |||
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita | : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita | ||
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao | |||
[http://people.chem.umass.edu/knapplab/?q=knappchem/index.html/ Knapp Lab] | |||
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010''' '''***New Fall 2014***''' | |||
: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky | |||
: | |||
: | |||
: '''[[Molecular Playground/ | |||
[http://www.chem.umass.edu/~cmartin/ Martin Lab] | [http://www.chem.umass.edu/~cmartin/ Martin Lab] | ||
: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia | : **'''[[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/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia | ||
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan | : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan | ||
[http://www.peytonlab.org/ Peyton Lab] | [http://www.peytonlab.org/ Peyton Lab] | ||
: | : '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''*** | ||
: '''[[Molecular Playground/MMP14]]''', Lauren Jansen | |||
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen | : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen | ||
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman | : '''[[Molecular Playground/FAK]]''', Dannielle Ryman | ||
| Line 150: | Line 98: | ||
: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino | : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino | ||
: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang | : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang | ||
: '''[[Molecular playground/Chymotrypsin]]''', Brad | : '''[[Molecular playground/Chymotrypsin]]''', Brad | ||
: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell | |||
[http://http://www.umass.edu/schiffman/ Schiffman Lab] | [http://http://www.umass.edu/schiffman/ Schiffman Lab] | ||
: | : '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger | ||
Tew Lab | Tew Lab | ||
: | : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde, Coralie Backlund | ||
Thayumanavan Lab | Thayumanavan Lab | ||
: | : '''[[Interleukin-1 beta]]''', Huan He | ||
: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez | : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez | ||
: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura | : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura | ||
: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi | : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi | ||
: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy | : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy | ||
: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado | : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado | ||
: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo | : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo | ||
: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko | : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko | ||
: '''[[Molecular Playground/MMP9]]''', Jiaming Zhuang, Mallory Gordon '''Revised 2014''' | |||
Thayumanavan & Vachet Labs | Thayumanavan & Vachet Labs | ||
| Line 197: | Line 127: | ||
[http://people.chem.umass.edu/thompson/index.html Thompson | [http://people.chem.umass.edu/thompson/index.html Thompson Lab] | ||
: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi '''"Revised 2014"''' | |||
: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin | |||
: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones | : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones | ||
: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li | |||
: | |||
[http://www.chem.umass.edu/~vachet/index.html Vachet Lab] | [http://www.chem.umass.edu/~vachet/index.html Vachet Lab] | ||
: | : **'''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano ''*Revised 2014*'' | ||
: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto, Tyler Marcinko ***'''Revised Fall 2014'''*** '''Best CBI Molecule Jmol scenes 2010''' | |||
: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto | |||
: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou | : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou | ||
:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne | |||
: '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang | |||
Vierling Lab | |||
: '''[[Molecular Playground/ | : '''[[Molecular Playground/sHSP]]''', Keith Ballard '''New 2014''' | ||
| Line 226: | Line 152: | ||
: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab] | : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab] | ||
Other Laboratories | |||
: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014''', Maroney Lab | |||
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr, Maroney Lab | |||
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014''', Maroney Lab | |||
: '''[[Molecular Playground/HypA]]''', Heidi Hu, Maroney Lab | |||
: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano, Chambers Lab | |||
:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab | :'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab | ||
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab | : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab | ||
: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab | : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab | ||
: '''[[Molecular Playground/CheR]]''', Miaomin Zhang, Forbes Lab | |||
: '''[[Molecular Playground/RBP]]''', Jan Panteli, Forbes Lab | |||
: '''[[Molecular Playground/TRAIL]]''', Charley Swofford, Forbes Lab | |||
: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab | : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab | ||
: '''[[Molecular Playground/Taxol]]''', Elizabeth Cummings, Rohan Patil, Sarah Wilson ***'''Revised Fall 2014'''***, Roberts Lab | |||
: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel, Roberts Lab | |||
: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab | : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab | ||
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab | : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab | ||
: '''[[Molecular Playground/Tic40]]''', Mine Canakci, Schnell Lab | |||
: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang, Holden Lab | |||
: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab] | : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab] | ||
| Line 250: | Line 191: | ||
'''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.''' | '''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 | Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind. | ||
A successful CBI Molecule | A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. 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. | 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 | 2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make. | ||
3. Get started working in Proteopedia. 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. Explore the HELP links below to learn how to make 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). | |||
'''Complete the above steps before the CBI Molecule Workshop.''' | |||
4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit 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 log in as themself and create a green scene to get credit for their work and to 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 2014" or "revised 2014". Minimize text; tell your story with green scenes! | |||
6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption). | |||
==Links to HELP pages== | ==Links to HELP pages== | ||
Latest revision as of 01:05, 16 July 2019
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 2014: CBI Molecules are due 12/3/14 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 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not). Follow the instructions at the bottom of this page.
MoleculesMolecules
** Designates CBI Molecules Featured on CBI website
- Molecular Playground/ClyA, Monifa Fahie, Bib Yang Revised 2014
- Molecular Playground/OmpG, Christina Chisholm, Monifa Fahie, Bib Yang Revised 2014
- Molecular Playground/ClpP, Lisa Hernandez, Rob Vass New 2014
- Molecular Playground/Homo-dimeric RcdA, Kamal K. Joshi
- **Molecular Playground/Hexameric ClpX, Joanne Lau Best CBI Molecule 2011
- Molecular Playground/DNA replication initiator DnaA, Jing Liu
Farkas Lab
- Molecular Playground/CLOCK:BMAL1 heterodimer complex, Hui-Hsien Lin, Joseph Hardie, Michael Mingroni New 2014
- Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon
- Molecular Playground/Human PPCA, Nilima Kolli
- Molecular_Playground/DnaK, Joseph Tilitsky, New 2014
- 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
- **Molecular_Playground/DHFR, Karan Hingorani Best CBI Molecule 2012
- 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-7 Dynamics
- 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/Hsp70-Hsp90, Jill Graham "Revised 2014"
- Molecular_Playground/ERDj5, Lydia Lamriben
- Molecular Playground/Saposin C, Abla Tannous
- Molecular_Playground/ERMan1, Johan Sunryd
- Molecular_Playground/Pcr H, Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang
- **Molecular Playground/Hemoglobin-Haptoglobin Complex, Ololade Fatunmbi, Chibueze Egeruoh ***New Fall 2014***
- Molecular Playground/Inteferon[Revised], Chengfeng Ren
- Molecular Playground/Transferrin, Khaja Muneeruddin, Jake Pawlowski
- Molecular Playground/Velaglucerase, Adriana Kita
- Molecular Playground/Antithrombin-Heparin, Yunlong Zhao
- Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin, Serap Pektas Best CBI Molecule Proteopedia Page 2010 ***New Fall 2014***
- Molecular Playground/FIH, Vanessa Chaplin, 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
- Molecular Playground/Human mtRNA pol, Ketan Mathavan
- Molecular Playground/IntegrinBeta1, Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***NEW FALL 2014'***
- Molecular Playground/MMP14, Lauren Jansen
- Molecular Playground/C-Raf, Thuy Nguyen
- Molecular Playground/FAK, Dannielle Ryman
- Molecular Playground/Reverse Transcriptase, Daniel Moyano-Marino
- Molecular Playground/Pancreatic Lipase, Rui Tang
- Molecular playground/Chymotrypsin, Brad
- Molecular Playground/Targeting Peptide, David Solfiell
- Molecular Playground/Streptavidin, Katrina Rieger
Tew Lab
- Molecular Playground/HIV Tat, Brittany deRonde, Coralie Backlund
Thayumanavan Lab
- 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/Gluconase, Jing Guo
- Molecular Playground/Glutathione Reductase, Reuben Chacko
- Molecular Playground/MMP9, Jiaming Zhuang, Mallory Gordon Revised 2014
Thayumanavan & Vachet Labs
- Molecular Playground/Trypsin, Gladys Murage
- Molecular Playground/Bacterial Chemotaxis Complex, Elizabeth R. Haglin, Maryam Kashefi "Revised 2014"
- Molecular Playground/CheA, Elizabeth R. Haglin
- Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones
- Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima, Xuni Li
- **Molecular Playground/Human Serum Albumin, Mahalia Serrano *Revised 2014*
- Molecular playground/beta 2 microglobulin, Nick Borotto, Tyler Marcinko ***Revised Fall 2014*** Best CBI Molecule Jmol scenes 2010
- Molecular Playground/Myoglobin, Yuping Zhou
- Molecular Playground/ Copper-Zinc Superoxide Dismutase, Shaynah Browne
- Molecular Playground/Ubiquitin salt bridge discussion, Zhe Zhang
Vierling Lab
- Molecular Playground/sHSP, Keith Ballard New 2014
Other Molecules of interest
- Molecular Playground/PcrA Helicase, Luis E Ramirez-Tapia, Martin Lab
Other Laboratories
- Molecular Playground/UreE, Priyanka Basak, New 2014, Maroney Lab
- Molecular Playground/Nickel Superoxide Dismutase, Carolyn Carr, Maroney Lab
- Molecular Playground/CsoR and RcnR, Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, Revised 2014, Maroney Lab
- Molecular Playground/HypA, Heidi Hu, Maroney Lab
- Molecular Playground/Glutamate Receptor, Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano, Chambers Lab
- Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp), Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
- Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
- Molecular Playground/ACP apo, Gitanjeli Prasad, Schnarr lab
- Molecular Playground/CheR, Miaomin Zhang, Forbes Lab
- Molecular Playground/RBP, Jan Panteli, Forbes Lab
- Molecular Playground/TRAIL, Charley Swofford, Forbes Lab
- Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor, Meili Yang, Weis lab
- Molecular Playground/Taxol, Elizabeth Cummings, Rohan Patil, Sarah Wilson ***Revised Fall 2014***, Roberts Lab
- Molecular Playground/Insulin, Whitney Stoppel, Roberts Lab
- Molecular Playground/Alginate-Fall2011, Joe White, David Griffi, Bhatia Lab
- Molecular Playground/Poly(ethylene glycol), Erika M. Saffer, Bhatia Lab
- Molecular Playground/Tic40, Mine Canakci, Schnell Lab
- Molecular Playground/Protective Antigen, Jing Huang, Holden Lab
- 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
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 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.
A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. 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, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.
3. Get started working in Proteopedia. 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. Explore the HELP links below to learn how to make 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).
Complete the above steps before the CBI Molecule Workshop.
4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit 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 log in as themself and create a green scene to get credit for their work and to 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 2014" or "revised 2014". Minimize text; tell your story with green scenes!
6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).
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.