Proteopedia - User contributions [en]

User:Jiaming Zhuang/Sandbox 2

2012-12-21T02:37:04Z

Jiaming Zhuang:

<Structure load='1gkc' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target. Various of <scene name='User:Jiaming_Zhuang/Sandbox_2/Ligand/1'>inhibitors</scene> have been designed to bind to the <scene name='User:Jiaming_Zhuang/Sandbox_2/Domain1/1'>catalytic domain</scene> and inhibit the activity of MMP9.

----
Reference:
Siân Rowsell, Paul Hawtin,Claire A. Minshull, Holly Jepson, Sarah M.V. Brockbank,Derek G. Barratt, Anthony M. Slater, William L. McPheat, David Waterson, Adriano M. Henney, Richard A. Pauptit Crystal Structure of Human MMP9 in Complex with a Reverse Hydroxamate Inhibitor, Volume 319, Issue 1, 24 May 2002, Pages 173–181
----

User:Jiaming Zhuang/Sandbox 2

2012-12-21T02:36:29Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-21T02:33:09Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-21T02:28:40Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-21T02:02:01Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-21T00:13:30Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-20T18:04:22Z

Jiaming Zhuang:

<Structure load='1L6J' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target. Various of [[inhibitors]] have been designed to bind to the [[catalytic domain]] and inhibit the activity of MMP9.

User:Jiaming Zhuang/Sandbox 2

2012-12-20T17:49:10Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-20T06:38:16Z

Jiaming Zhuang:

<Structure load='1gck' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target.

User:Jiaming Zhuang/Sandbox 2

2012-12-20T06:31:12Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-12-20T06:28:30Z

Jiaming Zhuang:

<Structure load='1gkc' size='500' frame='true' align='right' caption='Insert caption here' scene='MMP-9' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target.

User:Jiaming Zhuang/Sandbox 2

2012-12-20T06:06:55Z

Jiaming Zhuang: MMP-9 molecule

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target.

User:Jiaming Zhuang/Sandbox 2

2012-12-20T05:46:55Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2012-10-10T17:28:59Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9 complex/1'>MMP9</scene>

MMP9 is a member of matrix metalloproteinases (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target.

User:Jiaming Zhuang/Sandbox 2

2012-10-10T17:28:36Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9 complex/1'>MMP12</scene>

MMP9 is a member of matrix metalloproteinases (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target.

User:Jiaming Zhuang/Sandbox 2

2010-04-30T19:47:55Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp12/1'>MMP12</scene>

MMP12 is a member of matrix metalloproteinases (MMPs) which are zinc-dependent endopeptidases. Here, the complexation between the catalytic domain of human MMP12 and the inhibitor (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid is shown.

CBI Molecules

2010-04-30T19:44:38Z

Jiaming Zhuang:

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; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] laboratories

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

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

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

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

'''[[Molecular Playground/Taxol]]''', Rohan Patil

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

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

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

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

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

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

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

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

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', Chambers Lab (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

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

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

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

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

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.

CBI Molecules

2010-04-30T19:37:58Z

Jiaming Zhuang:

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; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Thompson & Weis laboratories

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

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

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

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

'''[[Molecular Playground/Taxol]]''', Rohan Patil

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

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

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

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

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

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

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

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

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', Chambers Lab (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

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

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

'''[[Molecular Playground/MMP]]''', Thai Lab, (Jiaming Zhuang)

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

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.

User:Jiaming Zhuang/Sandbox 2

2010-04-30T19:19:38Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2010-04-30T18:45:35Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-12/1'>TextToBeDisplayed</scene> The catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid

User:Jiaming Zhuang/Sandbox 2

2010-04-30T18:13:44Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2010-04-30T03:11:15Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />
<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/1'>TextToBeDisplayed</scene>

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/3'>TextToBeDisplayed</scene>

<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/4'>TextToBeDisplayed</scene>

User:Jiaming Zhuang/Sandbox 2

2010-04-30T03:09:53Z

Jiaming Zhuang:

User:Jiaming Zhuang/Sandbox 2

2010-04-30T03:09:15Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />
<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/1'>TextToBeDisplayed</scene>

User:Jiaming Zhuang/Sandbox 2

2010-04-30T03:08:20Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />
<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/1'>TextToBeDisplayed</scene>
<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/2'>TextToBeDisplayed</scene>

User:Jiaming Zhuang/Sandbox 2

2010-04-30T03:07:21Z

Jiaming Zhuang:

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />
<scene name='User:Jiaming_Zhuang/Sandbox_2/Mmp-9/1'>TextToBeDisplayed</scene>

User:Jiaming Zhuang/Sandbox 2

2010-04-30T02:28:43Z

Jiaming Zhuang: New page: <applet size='[450,338]' frame='true' align='right' caption='YYY' />

User:Jiaming Zhuang

2010-04-30T02:26:01Z

Jiaming Zhuang:

*[[User:Jiaming Zhuang/Sandbox 2]]