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References from Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly. Local targets link to admitted publications; unresolved targets remain external evidence.
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
RNA secondary structure analysis using RNAstructure
10.1002/cpz1.846 · 2023 · External reference
Scanfold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV
10.7717/peerj.6136/supp-15 · 2018 · External reference
ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes
10.7717/peerj.14361 · 2022 · External reference
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
10.1371/journal.pcbi.1012715 · 2024 · External reference
Probing binding hot spots at protein–RNA recognition sites
10.1093/nar/gkv876 · 2016 · External reference
Molecular architecture of protein-RNA recognition sites
10.1080/07391102.2015.1004652 · 2015 · External reference
ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
10.1261/rna.2125310 · 2010 · External reference
RNAalifold: improved consensus structure prediction for RNA alignments
10.1186/1471-2105-9-474 · 2008 · External reference
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
10.1093/nar/gkv1479 · 2016 · External reference
RNA-Puzzles Round V: blind predictions of 23 RNA structures
10.1038/s41592-024-02543-9 · 2025 · External reference
Physics-based de novo prediction of RNA 3D structures
10.1021/jp112059y · 2011 · External reference
Predicting RNA folding thermodynamics with a reduced chain representation model
10.1261/rna.2109105 · 2005 · External reference
Identification of RNA structures and their roles in RNA functions
10.1038/s41580-024-00748-6 · 2024 · External reference
Has AlphaFold3 achieved success for RNA?
10.1107/s2059798325000592 · 2025 · External reference
Rnadvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
10.1093/bib/bbae064 · 2024 · External reference
RNAcentral in 2026: genes and literature integration
10.1093/nar/gkaf1329 · 2026 · External reference
CONTRAfold: RNA secondary structure prediction without physics-based models
10.1093/bioinformatics/btl246 · 2006 · External reference
AlphaFold3 at CASP16
10.1002/prot.70044 · 2026 · External reference
A conserved viral RNA fold enables nuclease resistance across kingdoms of life
10.1093/nar/gkaf840 · 2025 · External reference
RNAZ 2.0: improved noncoding RNA detection
10.1142/9789814295291_0009 · 2009 · External reference
Prediction of locally stable RNA secondary structures for genome-wide surveys
10.1093/bioinformatics/btg388 · 2004 · External reference
Machine learning for RNA 2D structure prediction benchmarked on experimental data
10.1093/bib/bbad153 · 2023 · External reference
Structure modeling protocols for protein multimer and RNA in CASP16 with enhanced MSAs, model ranking, and deep learning
10.1002/prot.70033 · 2026 · External reference
NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation
10.1038/s41467-025-56261-7 · 2025 · External reference
Ligand binding prediction on pharmaceutical and nucleic acid targets by the CoDock group in CASP16
10.1002/prot.70032 · 2026 · External reference
Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers
10.1002/prot.70043 · 2026 · External reference
Assessment of nucleic acid structure prediction in CASP16
10.1002/prot.70072 · 2026 · External reference
Naturally ornate RNA-only complexes revealed by cryo-EM
10.1038/s41586-025-09073-0 · 2025 · External reference
Updates to the CASP infrastructure in 2024
10.1002/prot.70042 · 2026 · External reference
Critical assessment of methods of protein structure prediction (CASP)—round XV
10.1002/prot.26617 · 2023 · External reference
10.64898/2025.12.30.696949
10.64898/2025.12.30.696949 · 2025 · External reference
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences
10.1093/bioinformatics/btac426 · 2022 · External reference
ViennaRNA package 2.0
10.1186/1748-7188-6-26 · 2011 · External reference
DSSR: an integrated software tool for dissecting the spatial structure of RNA
10.1093/nar/gkv716 · 2015 · External reference
10.1093/nar/gkag813
10.1093/nar/gkag813 · 2026 · External reference
Improved RNA secondary structure prediction by maximizing expected pair accuracy
10.1261/rna.1643609 · 2009 · External reference
RNAspider: a webserver to analyze entanglements in RNA 3D structures
10.1093/nar/gkac218 · 2022 · External reference
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
10.1093/nar/gkaa1053 · 2020 · External reference
FARFAR2: improved de novo Rosetta prediction of complex global RNA folds
10.1016/j.str.2020.05.011 · 2020 · External reference
Protein structure prediction via deep learning: an in-depth review
10.3389/fphar.2025.1498662/xml · 2025 · External reference
Insights into RNA structure and function from genome-wide studies
10.1038/nrg3681 · 2014 · External reference
Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data
10.1016/j.str.2024.08.015 · 2024 · External reference
Unresolved reference
External reference
Infernal 1.1: 100-fold faster RNA homology searches
10.1093/bioinformatics/btt509 · 2013 · External reference
Critical assessment of AI-based protein structure prediction: fundamental challenges and future directions in drug discovery
10.1016/j.csbr.2025.100064 · 2025 · External reference
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions
10.1093/nar/gkae541 · 2024 · External reference
A structure-based model for the prediction of protein-RNA binding affinity
10.1261/rna.071779.119 · 2019 · External reference
When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines
10.1016/j.csbj.2025.10.003 · 2025 · External reference
Rfam 15: RNA families database in 2025
10.1093/nar/gkae1023 · 2025 · External reference
10.1101/2022.05.15.491755
10.1101/2022.05.15.491755 · 2022 · External reference
Automated 3D structure composition for large RNAs
10.1093/nar/gks339 · 2012 · External reference
RNA tertiary structure prediction using RNAComposer in CASP15
10.1002/prot.26578 · 2023 · External reference
CentroidFold: a web server for RNA secondary structure prediction
10.1093/nar/gkp367 · 2009 · External reference
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
10.1093/bib/bbad186 · 2023 · External reference
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
10.1093/bioinformatics/btr215 · 2011 · External reference
Unresolved reference
2015 · External reference
Accurate RNA 3D structure prediction using a language model-based deep learning approach
10.1038/s41592-024-02487-0 · 2024 · External reference
QRNAS: software tool for refinement of nucleic acid structures
10.1186/s12900-019-0103-1 · 2019 · External reference
RCSB protein data bank: delivering integrative structures alongside experimental structures and computed structure models
10.1093/nar/gkaf1187 · 2026 · External reference
Deep learning for RNA structure prediction
10.1016/j.sbi.2025.102991 · 2025 · External reference
trRosettaRNA: automated prediction of RNA 3D structure with transformer network
10.1038/s41467-023-42528-4 · 2023 · External reference
Cryo-EM reveals mechanisms of natural RNA multivalency
10.1126/science.adv3451 · 2025 · External reference
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
10.1016/j.jmb.2004.07.018 · 2004 · External reference
RNA 3D modeling with FARFAR2, online
10.1007/978-1-0716-2768-6_14 · 2023 · External reference
The RNA-puzzles assessments of RNA-only targets in CASP16
10.1002/prot.70052 · 2026 · External reference
Modeling of three-dimensional RNA structures using SimRNA
10.1007/978-1-0716-0708-4_6 · 2020 · External reference
Machine learning modeling of RNA structures: methods, challenges and future perspectives
10.1093/bib/bbad210 · 2023 · External reference
Enhancing RNA 3D structure prediction: a hybrid approach combining expert knowledge and computational tools in CASP16
10.1002/prot.70034 · 2026 · External reference
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement
10.1038/s41467-021-23100-4 · 2021 · External reference
Hierarchical assembly of RNA three-dimensional structures based on loop templates
10.1021/acs.jpcb.7b10102 · 2018 · External reference
Enhancing RNA 3D structure prediction in CASP16: integrating physics-based modeling with machine learning for improved predictions
10.1002/prot.26856 · 2026 · External reference
rMSA: a sequence search and alignment algorithm to improve RNA structure modeling
10.1016/j.jmb.2022.167904 · 2023 · External reference
