Hello Lina,

The output of MFOLD, or any other similar software package, is a list of base pairs, a list of interacting positions. Given an input sequence S of length n (S1,S2,S3,...,Sn), the secondary structure is a list of pairs, i:j, such that position i and j are predicted to form a base pair (A:T or T:A, G:C or CG, G:T or T:G [if wobble pairs are allowed]). The list will also satisfy other requirements, such the pairs are not crossing (no pseudo-knots), minimum distance between i and j, a position i can participate to only one base pair. Finally, over all possible secondary structures, MFLOD reports the one (the ones) with minimum free energy, according to a model, such as the nearest neighbour model.

As you can see, the output does not contain three-dimensional information. Consequently, you cannot simply convert the output to 3D (.pdb).

You need another software that takes as input the secondary structure information and predicts the three-dimensional structure (the coordinates (x,y,z) for all the atoms of all the nucleotides of your molecule).

Here are some references that should help you getting started with your project:

• Rother, K., Rother, M., Skiba, P. & Bujnicki, J. M. in RNA Sequence, Structure,and Function: Computationaland Bioinformatic Methods (eds. Gorodkin, J. & Ruzzo, W. L.) 1097, 395–415 (Humana Press, 2013).
• Dawson, W. K., Maciejczyk, M., Jankowska, E. J. & Bujnicki, J. M. Coarse-grained modeling of RNA 3D structure. Methods 103, 138–156 (2016).
• Boniecki, M. J. et al. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res 44, e63–e63 (2016).
• Biesiada, M., Pachulska-Wieczorek, K., Adamiak, R. W. & Purzycka, K. J. RNAComposer and RNA 3D structure prediction for nanotechnology. Methods 103, 120–127 (2016).
• Reinharz, V., Major, F. & Waldispühl, J. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 28, i207–i214 (2012).
• Dallaire, P. & Major, F. in RNA Sequence, Structure,and Function: Computationaland Bioinformatic Methods (eds. Gorodkin, J. & Ruzzo, W. L.) 1490, 237–251 (Springer New York, 2016).
• Cruz, J. A. et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18, 610–625 (2012).
• Parisien, M. & Major, F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452, 51–55 (2008).

[This list is obviously incomplete]

Hope this is useful.

All the best with your project!

Marcel

Hello Lina,

I have no experience with it but perhaps this might help:

https://www.webqc.org/molecularformatsconverter.php

Another way to go is perhaps you can translate the sequence into amino acid sequence:

For example use translate from expasy

Subsequently you can make a FASTA form out of your sequence and try I-Tasser (this will give you a 3D prediction in pdb form)

...just a thought. Good luck with your work.

Kind regards,

Rob

Good day Prof @Marcel Turcotte

Thank you very much for your explanation. Really appreciate your sharing as I'm a beginner in Bioinformatic. Tq once again Prof!

Good day Dr Rob Keller

Thank you for your feedback.

I've tried this website before but got an error message. I think i should check back my input in .ct file format. Anyway Tq very much Dr!

Firstly, get your structure file (in vennia format in it you can copy the sequence of your secondary structure) from http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAalifold.cgi

then visit

http://rnacomposer.cs.put.poznan.pl/

it accept maximum of 500nt.

Biesiada, M., Pachulska-Wieczorek, K., Adamiak, R. W. & Purzycka, K. J. RNAComposer and RNA 3D structure prediction for nanotechnology. Methods 103, 120–127 (2016).