# Are there Julia packages for RNA/DNA/protein structure prediction?

**URL:** <https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060>\
**Category:** Biology, Health, and Medicine\
**Tags:** package\
**Created:** [March 18, 2022, 1:00am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060 "2022-03-18T01:00:16Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![BetaQ](https://avatars.discourse-cdn.com/v4/letter/b/13edae/32.png) [@BetaQ](https://discourse.julialang.org/u/BetaQ)\
**Post date:** [March 18, 2022, 1:00am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/1 "2022-03-18T01:00:16Z")

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I am doing research about RNA and proteins. Therefore, I am looking for a method to simulate the secondary or 3D structure. I have used some methods based on other programming language constructs. But those methods are not very suitable for my projects.

I recently started learning Julia and found that Julia is a beautiful language. Based on Julia’s high efficiency, is there a suitable package for RNA or protein structural simulation? (like ViennaRNA for RNA or Alphafold for protein simulation)

Thanks! 😁

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**Author:** ![Sukera](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@Sukera](https://discourse.julialang.org/u/Sukera)\
**Post date:** [March 18, 2022, 2:13am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/2 "2022-03-18T02:13:51Z")

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This isn’t my field so I’m not familiar with all packages/features, but have you seen [https://biojulia.net/](https://biojulia.net/)?

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**Author:** ![trilobit](https://avatars.discourse-cdn.com/v4/letter/t/a8b319/32.png) [@trilobit](https://discourse.julialang.org/u/trilobit)\
**Post date:** [March 18, 2022, 8:51am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/3 "2022-03-18T08:51:39Z")

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[https://github.com/marcom/ViennaRNA.jl](https://github.com/marcom/ViennaRNA.jl)

For other packages you can search in the registry.I saw many packages  
for biological themes in general.

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<div class="post-metadata">

**Author:** ![BetaQ](https://avatars.discourse-cdn.com/v4/letter/b/13edae/32.png) [@BetaQ](https://discourse.julialang.org/u/BetaQ)\
**Post date:** [March 18, 2022, 9:42am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/4 "2022-03-18T09:42:48Z")

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Thanks for that link!  
BioStructures.jl and BioSequences.jl seem relatively relevant to my project. I am trying to use them in my project.  
Thank you!

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**Author:** ![BetaQ](https://avatars.discourse-cdn.com/v4/letter/b/13edae/32.png) [@BetaQ](https://discourse.julialang.org/u/BetaQ)\
**Post date:** [March 18, 2022, 9:47am UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/5 "2022-03-18T09:47:56Z")

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That might be something I am finding for. I will try it, thanks! 😀

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**Author:** ![lmiq](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lmiq/32/18314_2.png) [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Post date:** [March 18, 2022, 3:01pm UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/6 "2022-03-18T15:01:30Z")

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You won’t find anything “like AlphaFold”, but “we” (@gfahurbottino, my PhD student, actually) have developed a package to predict secondary structures and other one dimensional traits, here: [https://github.com/Hugemiler/TintiNet.jl](https://github.com/Hugemiler/TintiNet.jl)

The article is submitted for publication, maybe the infrastructure there serves as a inspiration. I think that could be adapted to predict RNA traits, what do you think, @gfahurbottino ?

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**Author:** ![kevbonham](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kevbonham/32/216165_2.png) [@kevbonham](https://discourse.julialang.org/u/kevbonham)\
**Post date:** [March 18, 2022, 3:07pm UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/7 "2022-03-18T15:07:26Z")

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You might also want to take a look at [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl), as well as [BioMakie.jl](https://github.com/kool7d/BioMakie.jl) for some plotting options

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**Author:** ![gfahurbottino](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gfahurbottino/32/34671_2.png) [@gfahurbottino](https://discourse.julialang.org/u/gfahurbottino)\
**Post date:** [March 18, 2022, 5:39pm UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060/8 "2022-03-18T17:39:25Z")

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Hi, BetaQ!

As @lmiq mentioned, we recently build a 100% julia-based (Flux.jl + Transformers.jl + BioJulia) sequence-structure translator. It’s based on a general encoder-decoder architecture, where the encoding block processes a sequence and the decoder block estimates properties.

In principle, you could use the same decoder architecture we built to train for Nucleic Acid secondary structures, rather than protein secondary structures. The training/evaluation scripts are available on the following repository (you probably want the `IGBT_classifier` version, for categorical secondary structures):

[https://github.com/Hugemiler/TintiNet.jl](https://github.com/Hugemiler/TintiNet.jl)