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PreprintCited by 41RNA and protein synthesis mechanismsProtein Structure and DynamicsRNA regulation and disease

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State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction

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Bernard, Clément, Postic, Guillaume, Ghannay, Sahar, Tahi, Fariza·2023·NAR Genomics and Bioinformatics
DOI 10.1101/2023.12.22.573067PMC PMC11091930

Preprint — published as 10.1093/nargab/lqae048 · Paper page

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Abstract

RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as either ab initio or template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but their adaptation to RNA 3D structure prediction remains difficult. In this paper, we give a brief review of the ab initio , template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine methods using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked methods, freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/state_of_the_rnart/

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Research works printed but not linked: 102

  1. 10.1038/s41419-022-05075-2 · DOI
  2. 10.1038/s41467-019-13494-7 · DOI
  3. 10.20892/j.issn.2095-3941.2018.0055 · DOI
  4. 10.1093/nar/28.1.235 · DOI · Paper page
  5. 10.1093/nar/gkaa1047 · DOI
  6. 10.1002/prot.25823 · DOI · Paper page
  7. 10.1038/s41586-019-1923-7 · DOI · Paper page
  8. 10.1093/nar/gkad726 · DOI
  9. 10.1042/BSR20180430 · DOI
  10. 10.3389/fgene.2020.574485 · DOI
  11. 10.3389/fmolb.2021.720937 · DOI
  12. 10.1021/acs.jcim.2c00939 · DOI
  13. 10.1529/biophysj.104.049239 · DOI
  14. 10.1103/PhysRevLett.128.108103 · DOI
  15. 10.1261/rna.1270809 · DOI
  16. 10.1093/bioinformatics/btn328 · DOI
  17. 10.1063/1.4881424 · DOI
  18. 10.1021/acs.jctc.5b00200 · DOI
  19. 10.1093/nar/gkv1479 · DOI
  20. 10.1021/acs.jctc.0c01148 · DOI
  21. 10.1021/acs.jpcb.1c07288 · DOI
  22. 10.1093/nar/gkad122 · DOI
  23. 10.1261/rna.047522.114 · DOI
  24. 10.1371/journal.pcbi.1000406 · DOI
  25. 10.1093/bioinformatics/btv221 · DOI
  26. 10.1016/0021-9991(77)90121-8 · DOI · Paper page
  27. 10.1063/1.1699114 · DOI · Paper page
  28. 10.1021/acs.jctc.7b01228 · DOI
  29. 10.1142/9789814295291_0024 · DOI
  30. 10.1093/nar/gkq1320 · DOI
  31. 10.1073/pnas.0703836104 · DOI
  32. 10.1016/j.str.2020.05.011 · DOI
  33. 10.1038/nature06684 · DOI
  34. 10.1093/nar/gks339 · DOI
  35. 10.1007/978-1-4939-7231-9_1 · DOI
  36. 10.1021/acs.jpcb.7b01933 · DOI
  37. 10.1038/srep00734 · DOI
  38. 10.3390/ijms20174116 · DOI
  39. 2020, 3dRNA: Building RNA 3D structure with improved template library, Comput Struct Biotechnol J, 18, 2416, 10.1016/j.csbj.2020.08.017 · DOI
  40. 10.1016/j.jmb.2022.167452 · DOI
  41. 10.1093/bioinformatics/btab292 · DOI
  42. 2022, FebRNA: an automated fragment-ensemble-based model for building RNA 3D structures, Biophysical Journal, 121, 3381, 10.1016/j.bpj.2022.08.017 · DOI
  43. 10.1016/j.jmb.2009.07.008 · DOI · Paper page
  44. 10.1021/jp110370s · DOI
  45. 10.1021/ja00315a051 · DOI
  46. 10.1529/biophysj.106.097782 · DOI
  47. 10.1261/rna.2109105 · DOI
  48. 10.1186/1471-2105-11-231 · DOI
  49. 10.1107/S0567739476001873 · DOI
  50. 10.1006/jmbi.1997.1284 · DOI
  51. 10.1016/S1090-7807(02)00014-9 · DOI
  52. 10.1093/nar/gkv141 · DOI
  53. 10.1093/nargab/lqad016.lqad016 · DOI
  54. 10.1016/0010-4809(89)90039-6 · DOI
  55. 10.1093/nar/gkab1074 · DOI
  56. 10.1038/s41467-021-21194-4 · DOI
  57. 10.1093/bib/bbad153 · DOI
  58. 10.1126/science.abe5650 · DOI
  59. 10.1371/journal.pcbi.1006011 · DOI
  60. 10.1021/acs.jcim.1c00153 · DOI
  61. 10.1101/2022.05.15.491755 · DOI
  62. 10.48550/arXiv.2207.01586 · DOI
  63. 10.1101/2023.09.20.558715 · DOI
  64. Ashish Vaswani , Noam Shazeer , Niki Parmar , Jakob Uszkoreit , Llion Jones , Aidan N Gomez , Łukasz Kaiser , and Illia Polosukhin . Attention is all you need. In I. Guyon , U. Von Luxburg , S. Bengio , H. Wallach , R. Fergus , S. Vishwanathan , and R. Garnett , editors, Advances in Neural Information Processing Systems, volume 30. Curran Associates, Inc., 2017.
  65. 10.1016/j.bpj.2023.10.011 · DOI
  66. 10.1038/s41467-023-41303-9 · DOI
  67. 10.1038/s41592-023-02086-5 · DOI · Paper page
  68. 10.1038/s41467-023-42528-4 · DOI
  69. 10.18653/V1/N19-1423 · DOI · Paper page
  70. 10.1093/nar/gky285 · DOI
  71. 10.1007/BF01589116 · DOI
  72. 10.1101/2022.08.06.503062 · DOI · Paper page
  73. 10.1073/pnas.1914677117 · DOI · Paper page
  74. 10.1038/s41596-021-00594-7 · DOI
  75. 10.1002/advs.202102592 · DOI
  76. 10.1038/s41467-019-13395-2 · DOI
  77. 10.1093/bioinformatics/btr215 · DOI
  78. 10.1016/j.jmb.2023.168210 · DOI
  79. 10.1371/journal.pcbi.1005659 · DOI · Paper page
  80. 10.1093/bib/bbae064 · DOI · Paper page
  81. 10.1093/nar/gkz1108 · DOI
  82. 10.1038/s41467-021-21194-4 · DOI
  83. 10.1093/bioinformatics/btac386 · DOI
  84. 10.1261/rna.031054.111 · DOI
  85. 10.1261/rna.049502.114 · DOI
  86. 10.1261/rna.060368.116 · DOI
  87. 10.1261/rna.075341.120 · DOI
  88. 10.1002/prot.26602 · DOI · Paper page
  89. 10.1261/rna.1700409 · DOI
  90. 10.1093/nar/gku972 · DOI
  91. 10.1002/prot.20264 · DOI · Paper page
  92. 10.1093/bioinformatics/btz282 · DOI
  93. 10.1093/bioinformatics/btt473 · DOI · Paper page
  94. 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W · DOI
  95. 10.1002/prot.24172 · DOI
  96. 10.1007/s10100-013-0296-5 · DOI
  97. 10.1261/rna.1837410 · DOI
  98. 10.1021/acs.jpcb.1c04584 · DOI
  99. 10.1002/pro.3235 · DOI · Paper page
  100. 10.1016/0022-2836(70)90057-4 · DOI · Paper page
  101. 10.1038/s41592-022-01585-1 · DOI · Paper page
  102. 10.1002/prot.26583 · DOI

Metadata

Authors
Bernard, C., Postic, G., Ghannay, S., & Tahi, F.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Université Paris-Saclay (FR)
Corresponding author
Tahi, Fariza
ORCID
Venue
NAR Genomics and Bioinformatics
Publisher
openRxiv
Published
2023-12-26
Volume
6
Issue
2
Pages
lqae048-lqae048
ISSN
2631-9268 (ISSN-L)
DOI
10.1101/2023.12.22.573067
PMC
PMC11091930
OpenAlex
W4396908238
Cited by
41
References
1
Citations by year
2026: 17 · 2025: 18 · 2024: 6
FWCI
5.57
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • NAR Genomics and Bioinformatics (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by-nc-nd)
  • HAL (submittedVersion)
Funders
  • Agence Nationale de la Recherche (ANR-11-IDEX-0003, ANR-11-LABX-0045, ANR-20, ANR-20-THIA-0013)
  • Grand Équipement National De Calcul Intensif (AD011014250)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
RNA 3D structure prediction, benchmarking, ab initio prediction, template-based modeling

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