User:Wayne Decatur/Sandbox

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<applet load='1rpu' size='400' frame='true' align='right' caption='p19 complexed with siRNA' />
Here is a schematic illustration of the two strands of this silencing RNA (siRNA):<br>
Here is a schematic illustration of the two strands of this silencing RNA (siRNA):<br>
<small><b><font face = 'courier'>
<small><b><font face = 'courier'>
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&nbsp;&nbsp;&nbsp;&nbsp;<font color = '#6060ff'>3'-OH-UUGCAUGCGCACUGCGCAUGCp-5'</font></font></b>
&nbsp;&nbsp;&nbsp;&nbsp;<font color = '#6060ff'>3'-OH-UUGCAUGCGCACUGCGCAUGCp-5'</font></font></b>
</small>
</small>
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{{STRUCTURE_1r9f | PDB= 1r9f | SCENE= }}
 
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<!--
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<scene name='User:Wayne_Decatur/Sandbox/Test/3'>TextToBeDisplayed</scene>
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The line below this paragraph, containing "STRUCTURE_1eve", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_1eve | PDB= 1eve | SCENE=Main_Page/E2020_in_ache_spinning/1 }}
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The collaborative, 3D encyclopedia of proteins and other molecules.
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===<span style="color:green">Green</span> links change the 3D image!===
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<big>''Here's an excerpt from one of our pages ([[1eve]]):''</big>
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The anti-Alzheimer's drug E2020 (marketed as Aricept&reg;) is an inhibitor that binds acetylcholinesterase (AChE) with high affinity. The X-ray structure of the E2020-AChE (AChE from ''Torpedo california'') complex shows that E2020 has a '''<scene name='1eve/E2020_close_up_with_84_279/12'>unique orientation</scene>''' along the active-site gorge, extending from the anionic subsite ('''<scene name='1eve/E2020_close_up_with_84lbld/6'>W84</scene>''') of the active site, at the bottom, to the peripheral anionic site ('''<scene name='1eve/E2020_close_up_with_84_279lbld/4'>near W279</scene>'''), at the top, via aromatic stacking interactions with conserved aromatic acid residues. E2020 does not, however, interact directly with either the catalytic triad or the 'oxyanion hole' but only '''<scene name='1eve/E20_interactionshown/7'>indirectly via solvent molecules</scene>'''.
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----
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[[Help:Protected_Pages|'''here''']] link with 3 quotes<br>
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[[Help:Protected_Pages|''here'']] link with 2 quotes<br>
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[[Help:Protected_Pages|here]] link with no quotes<br>
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==HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE==
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<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />
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T
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s, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.
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Here is the<br>
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<scene name='User:Wayne_Decatur/Sandbox/Test_animation/1'>test animation WAYNE made here on this page</scene>
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<!--HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE
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model 0;select all; spacefill on;
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that set up default display and then I loaded 2hty2hu4_j.pdb using load molecule under Scene authoring tools
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then in console, entered 'select 1.8' to select 8th model in file and then described how to display that particular model of the file that has 8 models:
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select 1.8; spacefill 0.2;wireframe 0.1; color red;
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anim mode palindrome;
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anim on;
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anim fps 8; # frames per second -->
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<scene name='User:Wayne_Decatur/Sandbox/Test_animation/3'>all in scene authoring tools with checked box</scene>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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</p>
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<p>&nbsp;</p>
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<p>&nbsp;</p>
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WEIRD thing with configuration I saw on October 24th 2009. When I enter 'configuration 1;' or 'configuration 2;' console in Proteopedia SAT, then it added weird lines from bases and among protein that were faint but I couldn't get rid of. It wouldn't happen in the newest version of FirstGlance linked to 1rpu page but then later it even wouldn't happen in SAT when I initiated new browser windows and JAVA runs. At first I thought it was leaving off the semi-colon but then it seemed to work with the semi-colon everywhere too. So another weird thing like when you need to scroll side of browser window to get a stuck animation going.
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<p>&nbsp;</p>
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==HOW TO on REFS==
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This is a sample <ref>Richardson DC, Richardson JS. The kinemage: a tool for scientific communication.
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Protein Sci. 1992 1:3-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1304880 1304880]</ref> of the
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standard references and one <ref>PMID:18673581</ref> with the PubmedID only new option <nowiki>"<ref>PMID:18673581</ref>"</nowiki>.
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It's possible now to have additional references by adding them to the group '''xtra'''.
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See this page source under ''Additional Literature and Resources''.
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== References ==
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<references/>
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== Additional Literature and Resources ==
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<ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref><ref group="xtra">PMID:16270100</ref><ref group="xtra">PMID:14661029</ref> <!--Putting all on one line eliminates blank space at top-->
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<references group="xtra"/>

Current revision

p19 complexed with siRNA

Drag the structure with the mouse to rotate

Here is a schematic illustration of the two strands of this silencing RNA (siRNA):
        5'-pCGUACGCGUCACGCGUACGUU-OH-3'
            |||||||||||||||||||
    3'-OH-UUGCAUGCGCACUGCGCAUGCp-5'


here link with 3 quotes
here link with 2 quotes
here link with no quotes

Contents

HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE

Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.

Drag the structure with the mouse to rotate

T s, , closer to the inhibitor.


Here is the



      

 

 


WEIRD thing with configuration I saw on October 24th 2009. When I enter 'configuration 1;' or 'configuration 2;' console in Proteopedia SAT, then it added weird lines from bases and among protein that were faint but I couldn't get rid of. It wouldn't happen in the newest version of FirstGlance linked to 1rpu page but then later it even wouldn't happen in SAT when I initiated new browser windows and JAVA runs. At first I thought it was leaving off the semi-colon but then it seemed to work with the semi-colon everywhere too. So another weird thing like when you need to scroll side of browser window to get a stuck animation going.

 

 

 

 

 

 

 

 

 

 

 

HOW TO on REFS

This is a sample [1] of the standard references and one [2] with the PubmedID only new option "<ref>PMID:18673581</ref>".

It's possible now to have additional references by adding them to the group xtra. See this page source under Additional Literature and Resources.

References

  1. ↑ Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Sci. 1992 1:3-9. PMID:1304880
  2. ↑ Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121

Additional Literature and Resources

  • Roth BM, Pruss GJ, Vance VB. Plant viral suppressors of RNA silencing. Virus Res. 2004 Jun 1;102(1):97-108. PMID:15068885 doi:http://dx.doi.org/10.1016/j.virusres.2004.01.020
  • Jabri E. Sizing up small RNAs. Nat Struct Mol Biol. 2004 Feb;11(2):112. PMID:14749769 doi:http://dx.doi.org/10.1038/nsmb0204-112
  • Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Sci. 1992 Jan;1(1):3-9. PMID:1304880
  • Lingel A, Simon B, Izaurralde E, Sattler M. The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double-stranded RNA recognition. EMBO Rep. 2005 Dec;6(12):1149-55. PMID:16270100
  • Ye K, Malinina L, Patel DJ. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature. 2003 Dec 18;426(6968):874-8. Epub 2003 Dec 3. PMID:14661029 doi:http://dx.doi.org/10.1038/nature02213

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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