User:ElNando888: Difference between revisions

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<p>This is&nbsp;<a href="http://eterna.cmu.edu/web/player/49507/" target="_blank">me on EteRNA</a>.</p>
<colgroup><col width="709"></col> </colgroup>  
<p>&nbsp;</p>
<tbody>
<p>Tip: while we're still working on the look and feel of this wiki, I would <strong>strongly</strong> suggest those using Chrome or Firefox to install the Stylish extension (if they haven't done so already), and to apply [http://userstyles.org/styles/86678/eterna-wiki-blue this stylesheet I composed myself]. Everything should feel much more comfortable. I certainly hope that we'll fix this properly in the future, but in the meantime, this could make the experience a little more enjoyable (it does for me).</p>
<tr height="19">
<p>&nbsp;</p>
<td class="et3" width="709" height="19">abc20180316</td>
<p>__TOC__</p>
</tr>
<p>&nbsp;</p>
<tr height="19">
<h2>My Groups</h2>
<td class="et3" width="709" height="19">http://www.pandorajewelryoutlet.in.net</td>
<ul>
</tr>
<li>[[The Spiral]]</li>
<tr height="19">
</ul>
<td class="et3" width="709" height="19">http://www.burberryoutlet.in.net</td>
<p>&nbsp;</p>
</tr>
<h2>Documents</h2>
<tr height="19">
<p>Written here on this wiki :</p>
<td class="et3" width="709" height="19">http://www.cheapmlbjerseys-wholesale.us.com</td>
<ul>
</tr>
<li>A [[/Blog|Blog]] about RNA in general</li>
<tr height="19">
<li>[[/Online meetings|Recorded online meetings]]</li>
<td class="et3" width="709" height="19">http://www.birkenstocksandalsuk.org.uk</td>
<li>Things specific to the [[/Static Cloud Labs|Static Cloud Labs]]</li>
</tr>
<li>Things specific to the [[/Switch Cloud Labs|Switch Cloud Labs]]</li>
<tr height="19">
<li>[[/Emscripten|Emscripten]]</li>
<td class="et3" width="709" height="19">http://www.pumashoesoutlet.us.com</td>
<li>[[/NF3 Tutorial|New Frontier 3 Tutorial]]</li>
</tr>
<li>[[/NF4 Discussion|New Frontier 4 Discussion]]</li>
<tr height="19">
</ul>
<td class="et3" width="709" height="19">http://www.monclerjacketssale.us.com</td>
<p>&nbsp;</p>
</tr>
<p>A few things I wrote as Google Docs :</p>
<tr height="19">
<ul>
<td class="et3" width="709" height="19">http://www.jacketscanadagoose.org.uk</td>
<li>[https://docs.google.com/file/d/0B8EEBMO3fRaUUkVNWWpRNEFPLVk/edit Switch Training Series 1.1 Walkthrough]</li>
</tr>
<li>[https://docs.google.com/file/d/0B8EEBMO3fRaUWVBEc3RqSUNhSFE/edit How to create FMN switch puzzles]</li>
<tr height="19">
<li>[https://docs.google.com/file/d/0B8EEBMO3fRaUTDFMSDdmZm5INm8/edit Quickstart with Chimera 1.7]</li>
<td class="et3" width="709" height="19">http://www.coachoutletus.us.com</td>
</ul>
</tr>
<p>&nbsp;</p>
<tr height="19">
<h2>Projects</h2>
<td class="et3" width="709" height="19">http://www.adidasyeezyshoes.us.com</td>
<ul>
</tr>
<li>[[/Vinnie|Vinnie]], a puzzle-solving, lab-designing bot.</li>
<tr height="19">
<li>[[/CBPP|CBPP]]</li>
<td class="et3" width="709" height="19">http://www.coachfactoryonlineoutlet.com.co</td>
<li>[[/Self-interacting sequences|Self-interacting sequences]]</li>
</tr>
<li>[[/Paper Lab: Riboswitches|Paper Lab: Riboswitches]]</li>
<tr height="19">
</ul>
<td class="et3" width="709" height="19">http://www.michael-korsoutlet.ca</td>
<p>&nbsp;</p>
</tr>
<h2>Links</h2>
<tr height="19">
<h3>3D structure prediction, visualization and design.</h3>
<td class="et3" width="709" height="19">http://www.pandoracharms-uk.org.uk</td>
<p>The online tools I like to use</p>
</tr>
<ul>
<tr height="19">
<li>[http://rnacomposer.ibch.poznan.pl/Home RNAComposer], ([http://rnacomposer.cs.put.poznan.pl/ mirror]), because it's real fast, even if it's far from perfect (see [[#Humor|the Humor section]])</li>
<td class="et3" width="709" height="19">http://www.cheapuggs.com.co</td>
<li>[http://www.cgl.ucsf.edu/chimera/ Chimera], because it's quite cheap ^^</li>
</tr>
</ul>
<tr height="19">
<p>&nbsp;</p>
<td class="et3" width="709" height="19">http://www.timberlandbootsoutlets.us.com</td>
<h3>Scientific papers</h3>
</tr>
<p>Not all I've read, but those that inspired ideas for my designs and for my bot Vinnie.</p>
<tr height="19">
<ul>
<td class="et3" width="709" height="19">http://www.canadagooseoutletjackets.us</td>
<li>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134247/ The non-Watson&ndash;Crick base pairs and their associated isostericity matrices]</li>
</tr>
<li>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280964/ Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function]</li>
<tr height="19">
<li>[http://dasher.wustl.edu/bio5357/reading/accchemres-44-xxx-11.pdf The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks]</li>
<td class="et3" width="709" height="19">http://www.doudounemonclerpascher.fr</td>
<li>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1170348/pdf/007490.pdf Solution structure of a GAAA tetraloop receptor&nbsp;RNA]</li>
</tr>
<li>[https://smartech.gatech.edu/handle/1853/44891?show=full RNA secondary structure prediction using a combined method of thermodynamics and kinetics]</li>
<tr height="19">
<li>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966716/ Thermodynamic Characterization of RNA Triloops]</li>
<td class="et3" width="709" height="19">http://www.pandora-jewelryoutlet.us.com</td>
<li>[http://rnajournal.cshlp.org/content/17/9/1688.full Correlating SHAPE signatures with three-dimensional RNA structures]</li>
</tr>
<li>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857344/ Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands]</li>
<tr height="19">
<li>[http://www.chem.unc.edu/rna/pdf-files/2011_ks_nprot.pdf Selective 2&prime;-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA]</li>
<td class="et3" width="709" height="19">http://www.coachfactoryoutletsonlines.us.com</td>
</ul>
</tr>
<p>&nbsp;</p>
<tr height="19">
<h3>Educational Resources</h3>
<td class="et3" width="709" height="19">http://www.christianlouboutinoutlet.us</td>
<ul>
</tr>
<li>[http://www.proteopedia.org/wiki/index.php/Main_Page Proteopedia]<br />Not really about RNA, but their usage of 3D interactive applets is awesome (see [http://www.proteopedia.org/wiki/index.php/Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase here] and [http://www.proteopedia.org/wiki/index.php/TRNA here]) and I would so very much like to have those tools here, on this wiki.&nbsp;</li>
<tr height="19">
</ul>
<td class="et3" width="709" height="19">http://www.oakley.nom.co</td>
<p>&nbsp;</p>
</tr>
<h3>Other</h3>
<tr height="19">
<ul>
<td class="et3" width="709" height="19">http://www.canadagoosesoutlet.ca</td>
<li>[http://www.begdb.com/ Benchmark Energy Geometry DataBase]<br />This is clearly violently hardcore. Probably only for physicists like Rhiju, or terminally addicted nutcases like Brourd and myself.&nbsp;</li>
</tr>
</ul>
<tr height="19">
<p>&nbsp;</p>
<td class="et3" width="709" height="19">http://www.birkenstockshoesoutlet.us.com</td>
<h2>Scratch Pad</h2>
</tr>
<ul>
<tr height="19">
<li>[[/WikiGetSat|GetSat replacement]]</li>
<td class="et3" width="709" height="19">http://www.raybanssunglassesoutlet.us.com</td>
<li>[[EteRNA/About EteRNA|About EteRNA]] (wikified, as well as a test of building a "wiki-path")</li>
</tr>
<li>[[User:Brourd/Loop Boosting Guide|Loop Boosting Guide]]</li>
<tr height="19">
<li>[[/Tests|Tests]]</li>
<td class="et3" width="709" height="19">http://www.adidas-yeezyboost.us.com</td>
</ul>
</tr>
<p>&nbsp;</p>
<tr height="19">
<h2>Humor</h2>
<td class="et3" width="709" height="19">http://www.canadiangoose.us.com</td>
<p>Warning: don't trust me with folding your [[What is RNA|RNA]], this is what happens when I try to play with [[nucleotide|nucleotides]] :</p>
</tr>
<p>&nbsp;</p>
<tr height="19">
<p>[[File:3Dfun_knot.png|frame|none|a knot...]]</p>
<td class="et3" width="709" height="19">http://www.outletlouisvuitton.us.com</td>
<p>&nbsp;</p>
</tr>
<p>[[File:3Dfun_zipper_accident.png|frame|none|a "zipper accident"...]]</p>
<tr height="19">
<p>&nbsp;</p>
<td class="et3" width="709" height="19">http://www.yeezyboost.org.uk</td>
<p>[[File:3Dfun_double_zipper.png|frame|none|pushing the limits, a double zipper accident!]]</p>
</tr>
<p>&nbsp;</p>
<tr height="19">
<p>[[File:3Dfun_ultrafolded.png|frame|none|Q: Why would you do a boring 1-2 internal loop, when you can make the most dramatic U-turn by passing a base-pair bond right in the middle of the stacking space of existing pairs?<br />A: You said to fold, right? This is as folded as it gets.]]</p>
<td class="et3" width="709" height="19">http://www.canadagooseukjackets.me.uk</td>
<p>&nbsp;</p>
</tr>
<p>[[File:3Dfun_spaghetti.png|frame|none|Something else with your RNA bolognese?]]</p>
<tr height="19">
<p>&nbsp;</p>
<td class="et3" width="709" height="19">http://www.coachoutletstoreonlineclearances.in.net</td>
<p>[[File:3Dfun_explosion.png|frame|none|and sometimes, the thing just explodes...]]</p>
</tr>
<p>&nbsp;</p>
<tr height="19">
<p>:D</p>
<td class="et3" width="709" height="19">http://www.cheapjordans.us.com</td>
<p><em>(nope, no special effects were required to take these shots)</em></p>
</tr>
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<td class="et3" width="709" height="19">http://www.monclerjacketsoutlet.in.net</td>
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<td class="et3" width="709" height="19">http://www.pandoracharms.com.co</td>
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<td class="et3" width="709" height="19">http://www.ralphlaurenoutletmalls.us.com</td>
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<td class="et3" width="709" height="19">http://www.monclerjacketsuk.org.uk</td>
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<td class="et3" width="709" height="19">http://www.michaelkorsoutletclearance.in.net</td>
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<td class="et3" width="709" height="19">http://www.canadagooseukjackets.org.uk</td>
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<td class="et3" width="709" height="19">http://www.michaelkorsfactoryoutletsale.us.com</td>
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</table>

Revision as of 08:12, 15 March 2018

This is <a href="http://eterna.cmu.edu/web/player/49507/" target="_blank">me on EteRNA</a>.

 

Tip: while we're still working on the look and feel of this wiki, I would strongly suggest those using Chrome or Firefox to install the Stylish extension (if they haven't done so already), and to apply this stylesheet I composed myself. Everything should feel much more comfortable. I certainly hope that we'll fix this properly in the future, but in the meantime, this could make the experience a little more enjoyable (it does for me).

 

 

My Groups

 

Documents

Written here on this wiki :

 

A few things I wrote as Google Docs :

 

Projects

 

Links

3D structure prediction, visualization and design.

The online tools I like to use

 

Scientific papers

Not all I've read, but those that inspired ideas for my designs and for my bot Vinnie.

 

Educational Resources

  • Proteopedia
    Not really about RNA, but their usage of 3D interactive applets is awesome (see here and here) and I would so very much like to have those tools here, on this wiki. 

 

Other

  • Benchmark Energy Geometry DataBase
    This is clearly violently hardcore. Probably only for physicists like Rhiju, or terminally addicted nutcases like Brourd and myself. 

 

Scratch Pad

 

Humor

Warning: don't trust me with folding your RNA, this is what happens when I try to play with nucleotides :

 

a knot...

 

a "zipper accident"...

 

pushing the limits, a double zipper accident!

 

Q: Why would you do a boring 1-2 internal loop, when you can make the most dramatic U-turn by passing a base-pair bond right in the middle of the stacking space of existing pairs?
A: You said to fold, right? This is as folded as it gets.

 

Something else with your RNA bolognese?

 

and sometimes, the thing just explodes...

 

:D

(nope, no special effects were required to take these shots)