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<big><big>Proposed Article Title: <big>'''Molecular Workbench'''</big>
<applet size='450' frame='true' align='right' caption='Insert caption here'
</big></big>
scene='User:Eric_Martz/Sandbox_6/2hu4_3cl0_aligned/4' />
{| align="left"
|-
| colspan="2"| &nbsp;
|-
| [[Image:Workbench-solo-small.gif]]
| width="100" | &nbsp;
|}


==What Is ''Molecular Workbench''?==
H274Y ([[Amino Acids#Histidine|Histidine]] to [[Amino Acids#Tyrosine|Tyrosine]]) is the most common mutation conferring resistance to the drug Tamiflu in the neuraminidase N1 of Influenza A (e.g. H1N1, H5N1). Although resistant, this mutant N1 still binds Tamiflu weakly, and a crystal structure was obtained, [[3ckz]]. Below, this is compared to the wild type, [[2hu4]]], using structural alignment of a single protein chain:Tamiflu complex from each.


The ''Molecular Workbench'' (MW) project offers free, '''ready-to-use educational activities''' as well as software for '''authoring'''<ref>Authoring ''Molecular Workbench'' Activities requires a substantial time commitment.</ref> such educational activities. The existing activities are primarily targeted to the middle and high school levels. College-level activities are under development. MW is the product of the [http://concord.org Concord Consortium]:
'''Why is the affinity of Tamiflu reduced by the mutation H274Y?''' Use the scenes below to help answer this question.
<blockquote>
&quot;The Concord Consortium is a nonprofit educational research and development organization based in Concord, Massachusetts. We create interactive materials that exploit the power of information technologies. Our primary goal in all our work is digital equity — improving learning opportunities for all students.&quot; ([http://concord.org Concord.Org])
</blockquote>
All software available from the Concord Consortium is
[http://mw.concord.org/modeler/faq.html#redistribute free and open-source].


Molecular Workbench activities are ''stand-alone'' programs (in [http://en.wikipedia.org/wiki/Java_(programming_language) java]). They run automatically and quickly from the MW website, and work equally well on Windows and Mac OS X.
Tamiflu is shown as thick sticks. Atoms contacting Tamiflu (4 &Aring;) are shown as balls. Amino acids that contain contacting atoms, plus amino acid 274, are shown as thin sticks. All other amino acids are hidden.


==What Can ''Molecular Workbench'' Do For Me?==
Influenza neuraminidase N1:
{| align="left"
|-
|[[Image:MW SAM.gif|left]]
|&nbsp;
|}


One of the newest parts of ''Molecular Workbench'' (MW) is the ''Science of Atoms and Molecules'' ([http://sam.concord.org SAM.Concord.Org]). It includes:
<jmol>
<jmolButton>
<script>anim off; frame 1.2</script>
<text>H274Y</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>anim off; frame 1.1</script>
<text>Wild Type</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>anim off; frame 0</script>
<text>Both</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>if (~animation); if (_animating); anim pause; else; anim mode loop 0 0;anim fps 2; anim resume; endif; endif;</script>
<text>Toggle Animation</text>
</jmolButton>
</jmol>


{| align="right"
Atoms are colored by element:
|-
{{Template:ColorKey_Element_C}},  
|
{{Template:ColorKey_Element_N}},
<imagemap>
{{Template:ColorKey_Element_O}} (in protein),
Image:MW Folding Simulations.gif|frame|<b>Protein folding simulations.</b> Click image for Movie.
<font color="magenta"><b>O</b></font> (in water).
default [[#Simulations: Protein Folding]]
</imagemap>
|}
* '''Simulations''' of biochemical, chemical and physical processes are featured. Often students can experiment by controlling parameters of the simulation.
 
* Protein and DNA molecules are '''interactive, rotating''' and change highlighted structural features in [[Jmol]].
<br clear="left">
{| align="left"
|-
|
<imagemap>
Image:MW_rover.png|left|frame|<b>Molecular Rover.</b> Click image for Movie.
default [[#Molecular Rover]]
</imagemap>
|}
* Students can pilot a '''Molecular Rover''' to explore the molecular structure structures of hemoglobin or immune system molecules (histocompatibility) to accomplish mission objectives. Some students find the Rover fun and engaging, while for others, learning how to pilot it is frustrating. Enthusiastic pilots could group with those who would rather not pilot. Only a handful of Activities utilize the Rover and these are optional -- most Activities do not use the Rover.
 
* Students '''capture snapshots''' of simulations, interactive molecules, or Rover explorations to document their achievements.
<!-- CAN'T GET THIS TO WORK
[[Image:MW_balloon.png|border|right|link=Morphs]]
-->
<imagemap>
Image:MW_balloon.png|right|frame|<b>Balloon Annotation.</b> Click image for Movie.
default [[#Balloons]]
</imagemap>
* Snapshot images can be '''annotated with balloons''', and '''described''' in open response text notes.
 
* SAM activities end by generating a '''report''' that includes answers to multiple choice questions, annotated snapshots, and the text of open responses. These reports are '''emailed to the teacher'''. Students have a chance to edit reports before they are submitted.
 
* Activities often include multiple choice questions that give '''immediate feedback''' to students. Encouraging '''hints''' can be given in response to incorrect answers.
 
* All activities can be '''downloaded for offline use''', in case your Internet connection is problematic.
{{Clear}}
<center>
{| class="wikitable" width="60%" style="background-color:#80ffff"
|-
|align="center"|<big>Assessment</big>
The immediate feedback and report-generating functions mentioned above provide assessment mechanisms for students and teachers.
|}
</center>
 
==How Do I Get Started?==
{| class="wikitable" align="right" style="background-color:#ffff80"
|-
| <big>Problems Running Molecular Workbench?</big>
* Make sure Java is installed: [http://molo.concord.org/software/ Help].
* Still not working? [http://molo.concord.org/software/overviewAndInstallation.htm#installCore More Help].
|}
Here are direct links to start a few MW SAM Activities that involve macromolecules (click '''Trust''' to permit each to start):
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/index.cml Four Levels of Protein Structure]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part1/protein3/index.cml Molecular Recognition & Protein Function]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/pna/index.cml Proteins and Nucleic Acids]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/dna/index.cml From DNA to Proteins]
 
Here is a direct link to see the entire list of dozens of SAM activities:
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part1/index.cml Science of Atoms and Molecules Activity Center]
 
To find the above list of SAM Activities from the Concord Consortium website:
# Start at [http://workbench.concord.org Workbench.Concord.Org], then
# Click on MW Curriculum.
# At the MW Database, click on SAM. (You can go here directly with [http://sam.concord.org SAM.Concord.Org].)
# At SAM, click on Activities, and '''Trust''' the java application.
# The MW application (a stand-alone java program) will start. Teachers who want to receive reports, and students who want to be able to send reports to their teacher, must register. If you just want to try the Activities '''without registering''', click on the link '''&quot;the public main page&quot;''' near the bottom.
# At the next MW page, click on '''Activity Center'''.
 
==Movies of Molecular Workbench==
 
Below are a few short movies that illustrate some capabilities of Molecular Workbench.
 
===Balloon Annotation===
<!--
[[Image:MW balloon.swf]]
-->
{| class="wikitable"
|-
| width="300"|Snapshots of simulations and interactive molecules enable students to report their findings. '''Balloons''' can be used to label snapshot images.
|<swf width="373" height="260">/wiki/images/8/8b/MW_balloon.swf</swf>
|}
 
===Simulations: Protein Folding===
This movie file is large (3 Mb) and <font color="red">may take a few minutes to download</font>. The movie will appear on the right below once download is complete.
{| class="wikitable"
|-
| width="300"|Students conduct experiments with simulations, record their findings in snapshots, and make reports.
|<swf width="373" height="260">/wiki/images/d/d1/MW_Protein_Folding_Sim.swf</swf>
|}
 
===Molecular Rover===
This movie file is large (10 Mb) and <font color="red">may take a few minutes to download</font>. The movie will appear on the right below once download is complete.
{| class="wikitable"
|-
| width="300"|The ''Molecular Rover'' is a vehicle that you can pilot to explore molecular structures. Here it is approaching a virus peptide (mostly <font color="green">green</font> and <font color="blue">blue</font>) attached to a histocompatibility protein on the surface of a cell. To try out the Rover, go to [http://rover.concord.org Rover.Concord.Org].
|<swf width="453" height="301">/wiki/images/8/82/MW_rover.swf</swf>
|}
 
==Notes==
<references />
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