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)
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
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 ?
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):
