Related Experiment Video
Updated: Jul 16, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
When will RNA get its AlphaFold moment?
Bohdan Schneider1, Blake Alexander Sweeney2, Alex Bateman2
1Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, CZ-252 50 Vestec, Czech Republic.
None:
The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches. We believe that there are challenges preventing the successful development of deep learning-based methods like AlphaFold for RNA in the short term. Broadly speaking, the challenges are the limited number of structures and alignments making data-hungry deep learning methods unlikely to succeed. Additionally, there are several issues with the existing structure and sequence data, as they are often of insufficient quality, highly biased and missing key information. Here, we discuss these challenges in detail and suggest some steps to remedy the situation. We believe that it is possible to create an accurate RNA structure prediction method, but it will require solving several data quality and volume issues, usage of data beyond simple sequence alignments, or the development of new less data-hungry machine learning methods.
More Related Videos
Related Concept Videos
RNA Stability
Nucleic Acid Structure
DNA Structure
DNA...
Bacterial Transcription
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Bacterial RNA Polymerase
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
RNA Editing
RNA Splicing

