RNA Tertiary Structure Modelling

All operations to build your own model you may find in small movie.

Two steps to fold coarse-grained model of RNA tertiary structure

Step #1:

  • fill in RNA secondary structure form with CT format (also with pseudoknots);
  • select helixes auto-stacking gap (see description below);
  • select short-distance tertiary interactions prediction (triples, "backside pentariples");
  • choose online representation of output structures;
  • push "Finish Step #1" button to obtain secondary and intermediate* structures.

* intermediate structure is the structure with minimum of "free energy" contains formed helixes and stacking, but without tertiary interactions


RNA secondary structure form
  • RNA should be shorter then 400 nucleotides!

  • You can paste any part of CT file into form, output structure numeration will start from the number 1.
    All interactions with unrepresented parts of the molecule will be discarded. So try to paste structural independent domains.

  • programm algorithm could process H-type pseudoknots!

  • secondary structure of RNA contains pseudoknots may be not plane

  • input CT should not contain tertiary interactions, please check it

  • for more details about CT format, look RNA Structure Formats

  • to convert bracket (Vienna) notation into CT, use converter (dose not support pseudoknots)

  • some useful RNA secondary structure databases:


Paste you structure in CT format here, or use "Sample CT"





Auto-stacking gap
  • GAP is a maximum distance in nucleotides of one strand between two helixes to perform coaxial stacking:

  • if one helix could generate several stacking forms with other helixes, it will form none; in that case please use manual stacking (Step #2).

stacking

0

1 or 0

      Include short-distance
tertiary interactions prediction
  • rRNA like triples A:(A:U) ; A:(G:C) ; A:(C:G) :

    penta
  • "backside pentariple" U:(C:G)(U:A) :

penta

Yes

No

Represent output structures in browser
  • required Java®:

  • may retard page downloading

Yes

No

Start first folding:

Versions: web interface v.1.0, software v.1.1
© 2008 Gleb Speshilov, Lomonosov Moscow State University