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When will RNA get its AlphaFold moment?

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 ma...

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Autores principales: Schneider, Bohdan, Sweeney, Blake Alexander, Bateman, Alex, Cerny, Jiri, Zok, Tomasz, Szachniuk, Marta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10570031/
https://www.ncbi.nlm.nih.gov/pubmed/37702120
http://dx.doi.org/10.1093/nar/gkad726
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author Schneider, Bohdan
Sweeney, Blake Alexander
Bateman, Alex
Cerny, Jiri
Zok, Tomasz
Szachniuk, Marta
author_facet Schneider, Bohdan
Sweeney, Blake Alexander
Bateman, Alex
Cerny, Jiri
Zok, Tomasz
Szachniuk, Marta
author_sort Schneider, Bohdan
collection PubMed
description 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.
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spelling pubmed-105700312023-10-14 When will RNA get its AlphaFold moment? Schneider, Bohdan Sweeney, Blake Alexander Bateman, Alex Cerny, Jiri Zok, Tomasz Szachniuk, Marta Nucleic Acids Res Critical Reviews and Perspectives 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. Oxford University Press 2023-09-13 /pmc/articles/PMC10570031/ /pubmed/37702120 http://dx.doi.org/10.1093/nar/gkad726 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Critical Reviews and Perspectives
Schneider, Bohdan
Sweeney, Blake Alexander
Bateman, Alex
Cerny, Jiri
Zok, Tomasz
Szachniuk, Marta
When will RNA get its AlphaFold moment?
title When will RNA get its AlphaFold moment?
title_full When will RNA get its AlphaFold moment?
title_fullStr When will RNA get its AlphaFold moment?
title_full_unstemmed When will RNA get its AlphaFold moment?
title_short When will RNA get its AlphaFold moment?
title_sort when will rna get its alphafold moment?
topic Critical Reviews and Perspectives
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10570031/
https://www.ncbi.nlm.nih.gov/pubmed/37702120
http://dx.doi.org/10.1093/nar/gkad726
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