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).
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
- New Frontier 3 Tutorial
- New Frontier 4 Discussion
A few things I wrote as Google Docs :
- Vinnie, a puzzle-solving, lab-designing bot.
- Self-interacting sequences
- Paper Lab: Riboswitches
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 ^^
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
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.
- Benchmark Energy Geometry DataBase
This is clearly violently hardcore. Probably only for physicists like Rhiju, or terminally addicted nutcases like Brourd and myself.
- GetSat replacement
- About EteRNA (wikified, as well as a test of building a "wiki-path")
- Loop Boosting Guide
(nope, no special effects were required to take these shots)