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<p>The online tools I like to use</p> | <p>The online tools I like to use</p> | ||
<ul> | <ul> | ||
<li>[http://rnacomposer.ibch.poznan.pl | <li>[http://rnacomposer.ibch.poznan.pl 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> | ||
<li>[http://www.cgl.ucsf.edu/chimera/ Chimera], because it's quite cheap ^^</li> | <li>[http://www.cgl.ucsf.edu/chimera/ Chimera], because it's quite cheap ^^</li> | ||
</ul> | </ul> |
Revision as of 07:39, 3 April 2020
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 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 :
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 :
:D
(nope, no special effects were required to take these shots)