RNA Composer 3D

Gameplay and Strategies Tools
1

RNA Composer is a new 3D modeling server available that claims fast, single processor results of superior accuracy. It runs in Poland and delivers a 3D rotating animation in jmol. It can accept sequence data only, or sequence & secondary structure in dot/bracket notation. Up to 500 nt in batch mode. Seems worth a look according to Brourd, and me.–eternacac

http://rnacomposer.ibch.poznan.pl/

2

Thanks for sharing the information eternacac…: )

janelle

3

The RNAComposer link is no longer working. I played with it for hours yesterday. It allowed me to render my EteRNA compositions in spinning 3D using Jmol. I also was able to screen grab a png of the folding shape of my “Boa Constrictor” puzzle. When you right-click on the Jmol viewer, you get scores of options for viewing the 3D molecule. My favourite is the ball and stick, stereographic crossed-eyed view with black background, absolutely brilliant.
I hope this is only a temporary problem.

4

After a bit of googling, I’ve found another link which seems to work:
http://rnacomposer.cs.put.poznan.pl/
Well worth exploring this site.
Use the “Copy the current sequence” button on EteRNA and paste it into the appropriate box in the rnacomposer page.
Then click Compose and wait a few minutes.
Click Jmol visualization and click and drag to see the 3D folding shape of the RNA
;):slight_smile:

5

I’m a big fan of this tool, and I find the exploration of those predicted 3D structures very inspiring and educational.

This said, anyone who uses it to create predictions should not forget that it is quite far from perfect. Current softwares are just decent at predicting 2D, but not so much for 3D (or if they are, it takes them orders of magnitude more time compared to this website).

For examples of what can go wrong with RNA Composer, see my humor section on EteRNA Wiki. And while you’re there, why not join the wiki and start contributing ? Thanks :slight_smile:

6

Weird–

I tried twice before to reply to Malcolm from my email and no dice, didn’t post here.

So, anyway, I’m glad you found it an an alternate path for when it goes down. It is pretty darned good and very fascinating to watch the RNA’s spin about in 3D.