RNA structure: advances and assessment of 3D structure prediction

Z Miao, E Westhof - Annual review of biophysics, 2017 - annualreviews.org
Biological functions of RNA molecules are dependent upon sustained specific three-
dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of …

When will RNA get its AlphaFold moment?

B Schneider, BA Sweeney, A Bateman… - Nucleic Acids …, 2023 - academic.oup.com
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 …

Assessment of three‐dimensional RNA structure prediction in CASP15

R Das, RC Kretsch, AJ Simpkin… - Proteins: Structure …, 2023 - Wiley Online Library
The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we
report assessments of RNA structure predictions in CASP15, the first CASP exercise that …

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

Y Li, C Zhang, C Feng, R Pearce… - Nature …, 2023 - nature.com
RNAs are fundamental in living cells and perform critical functions determined by their
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …

Has AlphaFold 3 reached its success for RNAs?

C Bernard, G Postic, S Ghannay, F Tahi - bioRxiv, 2024 - biorxiv.org
Predicting the 3D structure of RNA is a significant challenge despite ongoing advancements
in the field. Although AlphaFold has successfully addressed this problem for proteins, RNA …

[PDF][PDF] New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure

M Antczak, M Popenda, T Zok… - Acta Biochimica …, 2016 - frontierspartnerships.org
RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction,
freely available at http://rnacomposer. cs. put. poznan. pl/and http://rnacomposer. ibch …

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Z Miao, RW Adamiak, M Antczak, MJ Boniecki… - Rna, 2020 - rnajournal.cshlp.org
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka… - Rna, 2017 - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Z Miao, RW Adamiak, MF Blanchet, M Boniecki… - Rna, 2015 - rnajournal.cshlp.org
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment
in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10 …

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

M Magnus, M Antczak, T Zok, J Wiedemann… - Nucleic acids …, 2020 - academic.oup.com
Significant improvements have been made in the efficiency and accuracy of RNA 3D
structure prediction methods during the succeeding challenges of RNA-Puzzles, a …