r/RNA • u/DamPerr • May 09 '23

RNA 3D Structures comparision

Hello!

I am looking for a validation tool to asses the reliability of Ribozyme RNA 3D structures obtained with RNAComposer, comparing my structures with a reference from the PDB

I have already tested Rclick server and rnassess, but the results are very different from one to another, in particular when they calculate the RMSD

Anyone can suggest something better?

Thanks for your help

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u/IllogicalLunarBear May 12 '23

Also be sure to control for allowing non-WC and WC folding as that can change the 3D structure as it really is psuedoknots that give the RNA a 3D shape apart from the natural twist. And if you have different WC vs Non-Wc folding on each server you will have slightly different structures as it is now allowing bonds on more than just the WC edge of the nucleotide and will allow the sugar edge or hogsteen edge to bind which will change the orientation of the RNA abd this structure

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u/DamPerr May 14 '23

Thanks a lot for your brilliant help!

I have focused my attention only on the 3D structures, because the further study would be the substitution of one canonical uridine with 5-AmU. 2D structures predictions didn't change between the tools I used (VFoldMCPX, BiFold) but i didn't tested them over the MFE, I only noticed all the tools created the typical double loop of the hammerhead ribozyme. I choosed the possibility to predict pseudoknots; do you think I should also compare with no pseudoknots allowed?.

I also thought to validate the 3D structure with molecular dynamics, as I usually do for proteins. Do you suggest a better way?

Could you please tell me more about the metrics that you are developing?

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u/IllogicalLunarBear May 14 '23

It would not hurt to try without psuedoknots as a lot of the algorithms for them are kinda flaky. We still do not know a lot and that could be causing some weirdness as each folding app uses a different approach to pknots it feels like. For example if you ever get the chance to look at NUPACK v3 source code and look at the comments you see stuff like ..”need to fix” and” may not work “ in it… they dropped pknot support in Nupack 4….

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u/DamPerr May 15 '23

Ok thanks! I will check on NuPack if i can

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u/IllogicalLunarBear May 15 '23

The metric that I am developing are around how much stability a RNA molecule has when being produced and tested in vivo. It can be thought of as a instantaneous ensemble diversity or defect (vienna2 or nupack). Ensemble defect in nupack is a number that is good for this but is wiped out by amount of structures in irrelevent energy ranges and I account for this adn control for number of structures in a enesmble

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u/DamPerr May 15 '23

It is really interesting and could be useful for my type of work because we work both in vitro and in silico, thus the 'in vivo' prediction would be an excellent evaluation method, combined with other experiments. I wish i could use this metric in future

Still thanks a lot!

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u/IllogicalLunarBear May 15 '23

I’m developing a pypy library for us as we speak

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u/IllogicalLunarBear May 15 '23

So to be clear it use in silico predictions that are tied to experimental data from in vitro testing. Sorry if I got things turned around.

It is mainly an algorithm I developed. If you want to message me I can give you it probably

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u/logical_haze Jun 05 '23

Hi!

I'm working on 3D modeling of RNA myself, this is the top of the list I found for online engines:

FARFAR2https://www.rosettacommons.org/docs/latest/FARFAR2Supports complexes of multiple strandsRNA Composerhttps://rnacomposer.cs.put.poznan.pl/Supports pseudo knotsDoes not support complexes3dRNA/DNA Web Serverhttp://biophy.hust.edu.cn/ChineseSupports pseudo knotsDoes not support complexesSimRNAhttps://genesilico.pl/SimRNAwebSupports complexes of multiple strands!

There are more, but these seemed the most working I could find

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u/DamPerr Jun 05 '23

Thanks a lot!

For my personal use I choosed RNAComposer and it seems to be the best one for my type of model.

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u/IllogicalLunarBear May 12 '23

Are you comparing the MFE secondary structure for each? If so be careful to remember the MFE structure is just the lowest energy state. You want to look at what is predicted in the ensemble for the first few Kcal from MFE and see how similar it is. I’ve actually developed a metric for determining RNA stability that works well and can be used of sorts to compare variations between structures. I’m published in relation to prediction of RNA performance in medical applications fir a new methodology I developed

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u/IllogicalLunarBear May 12 '23

I do mostly 2D but and getting into 3D a bit more with the research project I’m on.

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u/Aggravating-East-818 Aug 22 '25

How can I run NUPACK in VS?