User:ElNando888

This is me on EteRNA.

 

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

• The Spiral

 

Documents

Written here on this wiki :

• A Blog about RNA in general
• Recorded online meetings
• Things specific to the Static Cloud Labs
• Things specific to the Switch Cloud Labs
• Emscripten
• New Frontier 3 Tutorial
• New Frontier 4 Discussion

 

A few things I wrote as Google Docs :

• Switch Training Series 1.1 Walkthrough
• How to create FMN switch puzzles
• Quickstart with Chimera 1.7

 

Projects

• Vinnie, a puzzle-solving, lab-designing bot.
• CBPP
• Self-interacting sequences
• Paper Lab: Riboswitches

 

Links

3D structure prediction, visualization and design.

The online tools I like to use

• RNAComposer, (mirror), because it's real fast, even if it's far from perfect (see the Humor section)
• Chimera, because it's quite cheap ^^

 

Scientific papers

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

• The non-Watson–Crick base pairs and their associated isostericity matrices
• Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function
• The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks
• Solution structure of a GAAA tetraloop receptor RNA
• RNA secondary structure prediction using a combined method of thermodynamics and kinetics
• Thermodynamic Characterization of RNA Triloops
• Correlating SHAPE signatures with three-dimensional RNA structures
• Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands
• Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA

 

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

• GetSat replacement
• About EteRNA (wikified, as well as a test of building a "wiki-path")
• Loop Boosting Guide
• Tests

 

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)