Proteopedia - User contributions [en]

User:Daniel Seeman

2020-06-02T19:34:34Z

Daniel Seeman:

<center>'''[https://www.linkedin.com/in/daniel-seeman Daniel P. Seeman, PhD (Senior Scientist)]'''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component of both protein self-association, ''and'' interactions with bio-derived polyelectrolytes.]]

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2020-06-02T19:31:39Z

Daniel Seeman:

<center>'''[https://www.linkedin.com/in/daniel-seeman Daniel P. Seeman, PhD (Senior Scientist)]'''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component of both protein self-association, ''and'' interactions with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2020-06-02T19:31:12Z

Daniel Seeman:

<center>'''[http://www.linkedin.com/in/daniel-seeman Daniel Seeman, PhD]'''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component of both protein self-association, ''and'' interactions with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2020-06-02T19:30:38Z

Daniel Seeman: Update current affiliation/title

<center>'''[linkedin.com/in/daniel-seeman Daniel Seeman, PhD]'''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component of both protein self-association, ''and'' interactions with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:52:01Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component of both protein self-association, ''and'' interactions with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:51:19Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of three proteins (β-lactoglobulin, Bovine serum albumin, and Zn-Insulin) at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component in both protein self-association and interaction with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:51:00Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera. Protein charge anisotropy is a major component in both protein self-association and interaction with bio-derived polyelectrolytes.]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:50:03Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:49:19Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin shown at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:49:00Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|center|thumb|400px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin shows at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:45:24Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|300px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin shows at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:45:12Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''

[[Image:delphiproteins.png|300-px|Electrostatic potentials of β-lactoglobulin, Bovine serum albumin, and Zn-Insulin shows at pH 6. Calculated with DelPhi (a 'Nonlinear Poisson Boltzmann Solver') and displayed using UCSF Chimera]]

</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:42:00Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''
</center>

[[Image:delphiproteins.png|Y. Xu, D. Seeman, Y. Yan, L. Sun, J. Post, P.L. Dubin. “Effect of Heparin on Protein Aggregation: Inhibition versus Promotion”. Biomacromolecules, 13 (2012), 1642-1651]]

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

File:Delphiproteins.png

2014-01-29T16:41:38Z

Daniel Seeman: From ''Y. Xu, D. Seeman, Y. Yan, L. Sun, J. Post, P.L. Dubin. “Effect of Heparin on Protein Aggregation: Inhibition versus Promotion”. Biomacromolecules, 13 (2012), 1642-1651''. Not sure if this is ok to upload .. if not, let me know. It's from an A

From ''Y. Xu, D. Seeman, Y. Yan, L. Sun, J. Post, P.L. Dubin. “Effect of Heparin on Protein Aggregation: Inhibition versus Promotion”. Biomacromolecules, 13 (2012), 1642-1651''.

Not sure if this is ok to upload .. if not, let me know. It's from an ACS journal, I'm a coauthor on the paper, and I made this figure. 18:41, 29 January 2014 (IST)

User:Daniel Seeman

2014-01-29T16:32:44Z

Daniel Seeman:

<center>'''[https://people.chem.umass.edu/dseeman/ Daniel Seeman - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Dubin Research Group at the University of Massachusetts-Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2014-01-29T16:30:40Z

Daniel Seeman:

<center>''I am a Ph.D. Candidate in the Chemistry Department at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

User:Daniel Seeman

2013-05-02T00:11:27Z

Daniel Seeman:

User:Daniel Seeman

2013-05-02T00:11:12Z

Daniel Seeman:

<center>''I am a Ph.D. Candidate in the Chemistry Department at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2013-05-01T23:56:11Z

Daniel Seeman:

<center>'''[http://people.chem.umass.edu/dubinlab/dubin_members.html#Daniel Daniel Seeman - Dubin Lab Homepage - UMass - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Chemistry Department at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2013-05-01T23:47:23Z

Daniel Seeman:

<center>'''[http://people.chem.umass.edu/dubinlab/dubin_members.html Daniel Seeman - Dubin Lab Homepage - UMass - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Chemistry Department at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2013-05-01T23:47:05Z

Daniel Seeman:

<center>'''[http://people.chem.umass.edu/dubinlab/dubin_members.html Daniel Seeman - Dubin Lab Homepage - UMass - Department of Chemistry]'''
''I am a Ph.D. Candidate in the Department of Chemistry at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2013-05-01T23:46:50Z

Daniel Seeman:

<center>'''[http://people.chem.umass.edu/dubinlab/dubin_members.html Daniel Seeman - Dubin Lab Homepage - UMass - Department of Chemistry - People]'''
''I am a Ph.D. Candidate in the Department of Chemistry at the University of Massachusetts, Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2012-07-12T18:39:36Z

Daniel Seeman:

<center>[[User:Daniel Seeman|Daniel Seeman]]
''I am a Ph.D. Candidate in the Chemistry Department at the University of Massachusetts Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2012-05-17T13:08:22Z

Daniel Seeman: chemwiki no longer online

<center>[[User:Daniel Seeman|Daniel Seeman]]
''I am a PhD Candidate in the Chemistry Department at the University of Massachusetts Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2012-05-17T13:07:28Z

Daniel Seeman: no more umass chem wiki

<center>[[User:Daniel Seeman|Daniel Seeman]]
 ''I am a PhD Candidate in the Chemistry Department at the University of Massachusetts Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman

2012-03-29T17:33:26Z

Daniel Seeman:

<center>[[User:Daniel Seeman|Daniel Seeman]]
 '''[https://people.chem.umass.edu/wiki/index.php?title=User:Dseeman My User Page on the Umass Chem Wiki]'''
 ''I am a PhD Candidate in the Chemistry Department at the University of Massachusetts Amherst''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

User:Daniel Seeman/DELETE

2011-03-29T19:53:54Z

Daniel Seeman: User:Daniel Seeman/Caspases moved to User:Daniel Seeman/-

User:Daniel Seeman/DELETE

2011-03-29T19:53:43Z

Daniel Seeman: Replacing page with '-'

CBI Molecules

2010-12-10T14:01:24Z

Daniel Seeman:

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

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

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

: '''[[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

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

[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

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/Caspase-6 (new)

2010-12-10T14:00:48Z

Daniel Seeman: Elih Velazquez fall 2010

Caspase-6 is a [[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].

== Caspase-6 ==

<Structure load='3OD5' size='500' frame='true' align='right' caption='Liganded Caspase-6, with active site inhibitor' />

Caspase-6 has been found to have a critical role in neurodegeneration diseases like Alzheimer's and Huntington. The experimental evidence is based on transgenic mice as well as in vitro studies.

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/Caspase-6

2010-12-10T14:00:11Z

Daniel Seeman:

Caspase-6 is a [[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].

== Caspase-6 ==

<applet scene='User:Daniel_Seeman/Workbench/C6forelih/1' load='2WDP' size='300' frame='true' align='right' caption='Caspase-6 from pdb 2WDP' />

Caspase-6 has been found to have a critical role in neurodegeneration diseases like Alzheimer's and Huntington. The experimental evidence is based on transgenic mice as well as in vitro studies.

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/Caspase-6

2010-12-10T13:59:14Z

Daniel Seeman: Elih Velazquez update

CBI Molecules

2010-12-10T13:47:27Z

Daniel Seeman:

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

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]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

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

: '''[[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

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

[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

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.

User:Daniel Seeman

2010-12-10T13:44:44Z

Daniel Seeman:

<center>[[User:Daniel Seeman|Daniel Seeman]]
 '''[https://people.chem.umass.edu/wiki/index.php?title=User:Dseeman My User Page on the Umass Chem Wiki]'''
 ''I am a graduate student at the University of Massachusetts Amherst Chemistry Department''
</center>

=== About proteopedia: ===
:'''Topic Pages''': articles
:'''green links''': animations/scenes
:'''PDB seed''': automatically generated page for pdb files.
:'''User pages''': ''this'' page, and others like it

=== new page(s): ===
*[[User:Daniel Seeman/Alpha-1-antitrypsin]]
*[[User:Daniel Seeman/Caspase-7 Dynamics]]
*[[Alpha-1-antitrypsin]]
*[[Molecular_Playground/BLG]]

Molecular Playground/BLG

2010-12-10T13:44:13Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB' size='500' frame='true' align='right' caption='BLG A and BLG B are isoforms that differ by 2 charge units' scene='Molecular_Playground/BLG/Blgscene/1' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

Molecular Playground/BLG

2010-12-10T13:43:03Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

=== BLG dimer turn ===

<scene name='Molecular_Playground/BLG/Blgscene/1'>BLG dimer</scene>

Molecular Playground/BLG

2010-12-10T13:42:43Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.
<scene name='Molecular_Playground/BLG/Blgscene/1'>BLG dimer</scene>

Molecular Playground/BLG

2010-12-10T13:41:30Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB' name='Molecular_Playground/BLG/Blgscene/1' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

Molecular Playground/BLG

2010-12-10T13:37:21Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

Molecular Playground/BLG

2010-12-10T13:37:09Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

<Structure load='1BEB.pdb' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

Molecular Playground/BLG

2010-12-10T13:36:20Z

Daniel Seeman:

β-lactoglobulin is a [[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].

=== BLG as studied in the Dubin Lab ===

β-lactoglobulin is a dimeric protein that exists in two forms. BLG A and BLG B, which differ by two mutations, one of which is a non-charged residue being replaced by an Aspartic Acid, which at relevant pH values is negatively charged. The result is a protein that exists in two isoforms, which differ by two negative charges (one per monomer).

The differences between these two forms significantly augment the electrostatic potential, making BLG A & BLG B an ideal system for studying the interaction of a protein with a polyelectrolyte.

Molecular Playground/BLG

2010-12-10T13:34:25Z

Daniel Seeman:

Molecular Playground/BLG

2010-12-10T13:30:13Z

Daniel Seeman: New page: β -lactoglobulin is a CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]<...

Molecular Playground/Caspase-6

2010-05-12T14:46:46Z

Daniel Seeman:

Caspase-6 is a [[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].

== Caspase-6 ==

<applet scene='User:Daniel_Seeman/Workbench/C6forelih/1' load='2WDP' size='300' frame='true' align='right' caption='Caspase-6 from pdb 2WDP' />

Caspase-6 has been found to have a critical role in neurodegeneration diseases like Alzheimer's and Huntington. The experimental evidence is based on transgenic mice as well as in vitro studies.

Molecular Playground/Caspase-6

2010-05-12T14:34:22Z

Daniel Seeman:

Caspase-6 is a [[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].

== Caspase-6 ==

<applet scene='User:Daniel_Seeman/Workbench/C6forelih/1' load='2WDP' size='300' frame='true' align='right' caption='Caspase-6 from pdb 2WDP' />

Caspases are proteases critical to apoptosis. Apoptosis can be initiated through either an intrinsic or extrinsic pathway.

CBI Molecules

2010-05-12T14:30:16Z

Daniel Seeman:

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.

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

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

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

: '''[[Molecular Playground/Caspase-7 Dynamics]]''', Daniel Seeman

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

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

: '''[[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
: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia

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

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

: '''[[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

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

Vachet Lab

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick

Other UMass labs

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

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.

Molecular Playground/Caspase-6

2010-05-12T14:29:03Z

Daniel Seeman: page created with Daniel's account (Elih's page)