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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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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. |
format | Online Article Text |
id | pubmed-10570031 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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