Proteopedia - User contributions [en]

Molecular Playground/Dengue Virus Protease

2012-01-10T23:03:53Z

Muslum Yildiz:

<Structure load='2fom' size='500' frame='true' align='right' caption='Dengue virus protease has crucial role in dengue virus life cycle.' scene='' />
Dengue Virus Protease is a CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
Dengue virus protease has crucial role in dengue virus life cycle. Dengue virus cause Dengue Fever disease which is the most important tropical disease after Malaria and according WHO resources 2.5 billion people worldwide are at the risk of infection.50milion infection cases are reported each year and Dengue fever is now endemic in 100 countries including Americas where 890.000 infection cases are reported in 2007 alone. (WHO)

<scene name='Molecular_Playground/Dengue_Virus_Protease/Scenename/2'>Click on Green Link to change display style!</scene>

Molecular Playground/Dengue Virus Protease

2012-01-10T23:03:06Z

Muslum Yildiz:

Molecular Playground/Dengue Virus Protease

2012-01-10T23:01:17Z

Muslum Yildiz:

<Structure load='2fom' size='500' frame='true' align='right' caption='Dengue virus protease has crucial role in dengue virus life cycle.' scene='' />
Dengue Virus Protease is a CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
Dengue virus protease has crucial role in dengue virus life cycle. Dengue virus cause Dengue Fever disease which is the most important tropical disease after Malaria and according WHO resources 2.5 billion people worldwide are at the risk of infection.50milion infection cases are reported each year and Dengue fever is now endemic in 100 countries including Americas where 890.000 infection cases are reported in 2007 alone. (WHO)

Copy and paste the following line where you want the scene link to appear (scroll down if needed) and edit the TextToBeDisplayed:

<scene name='Molecular_Playground/Dengue_Virus_Protease/Scenename/2'>TextToBeDisplayed</scene>

Molecular Playground/Dengue Virus Protease

2012-01-10T22:56:07Z

Muslum Yildiz:

Molecular Playground/Dengue Virus Protease

2012-01-10T22:55:44Z

Muslum Yildiz:

<Structure load='2fom.pdb' size='500' frame='true' align='right' caption='Dengue virus protease has crucial role in dengue virus life cycle.' scene='' />
Dengue Virus Protease is a CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
Dengue virus protease has crucial role in dengue virus life cycle. Dengue virus cause Dengue Fever disease which is the most important tropical disease after Malaria and according WHO resources 2.5 billion people worldwide are at the risk of infection.50milion infection cases are reported each year and Dengue fever is now endemic in 100 countries including Americas where 890.000 infection cases are reported in 2007 alone. (WHO)

Molecular Playground/Dengue Virus Protease

2011-03-10T21:47:50Z

Muslum Yildiz:

Dengue Virus Protease is a CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
Dengue virus protease has crucial role in dengue virus life cycle. Dengue virus cause Dengue Fever disease which is the most important tropical disease after Malaria and according WHO resources 2.5 billion people worldwide are at the risk of infection.50milion infection cases are reported each year and Dengue fever is now endemic in 100 countries including Americas where 890.000 infection cases are reported in 2007 alone. (WHO)
[[Image:2fom dvp2.png|thumb|Dengue virus protease has crucial role in dengue virus life cycle.]]

Molecular Playground/Dengue Virus Protease

2011-03-10T21:46:04Z

Muslum Yildiz:

Molecular Playground/Dengue Virus Protease

2011-03-10T21:45:45Z

Muslum Yildiz:

Dengue Virus Protease is a [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

[[Image:2fom dvp2.png|thumb|stuff]]

Molecular Playground/Dengue Virus Protease

2011-03-10T21:45:03Z

Muslum Yildiz:

[[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

[[Image:2fom dvp2.png|thumb|stuff]]

Molecular Playground/Dengue Virus Protease

2011-03-10T21:43:26Z

Muslum Yildiz: Replacing page with 'Image:2fom dvp2.png'

[[Image:2fom dvp2.png]]

CBI Molecules

2011-03-10T21:42:35Z

Muslum Yildiz:

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2010: New entries are due 12/10/10. Please append the designation (new Fall 2010) to your new entries. If you want to build on a previous entry, 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.

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau (new Fall 2010)

Forbes Lab

: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[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
:: Best Overall CBI Molecule 2010

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[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/ERMan1]]''', Johan Sunryd

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

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

[http://robertsgroup.ecs.umass.edu/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

Schnarr Lab

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado

: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

Instructions:

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecules page and/or scene will be awarded in spring 2011!'''

Choose a molecule that is part of your research project.

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. 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.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. 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."

6. 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.

7. 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 "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

Molecular Playground/Dengue Virus Protease

2011-03-10T21:42:17Z

Muslum Yildiz: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}