ArticleProteins2026
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.
Abstract read
In one paragraph
Article in Proteins, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Molecular insights into dynamic RNA quaternary assemblies.RNA biology · 2026Review
- ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.Journal of molecular biology · 2026Article
- Reconsidering Molecular Docking Practices in Aptamer Research.Chembiochem : a European journal of chemical biology · 2026Article
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.Nature communications · 2026Article
- Single-round evolution of RNA aptamers with GRAPE-LM.Nature biotechnology · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction.Proteins · 2026Review
- Modeling Alternative Conformational States in CASP16.Proteins · 2026Article
- ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces.Computational and structural biotechnology journal · 2026Article
- Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.Proteins · 2026Article
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Article
- Template-based RNA structure prediction advanced through a blind code competition.bioRxiv : the preprint server for biology · 2025Article
- Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.Nucleic acids research · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Modeling Alternative Conformational States in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Graph neural network and diffusion model for modeling RNA interatomic interactions.Bioinformatics (Oxford, England) · 2025Article
Corrections and comments
- Update of
Authors and funding
33 authors.
Rachael C KretschBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID https://orcid.org/0000-0002-6935-518X
Reinhard AlbrechtDepartment of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
Ebbe S AndersenDepartment of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.ORCID https://orcid.org/0000-0002-6236-8164
Hsuan-Ai ChenInstitute of Organic Chemistry and Center for Nanosystems Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.ORCID https://orcid.org/0000-0002-0586-0742
Wah ChiuBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID https://orcid.org/0000-0002-8910-3078
Rhiju DasBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID https://orcid.org/0000-0001-7497-0972
Jeanine G GezelleDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.ORCID https://orcid.org/0000-0003-3664-6199
Marcus D HartmannDepartment of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.ORCID https://orcid.org/0000-0001-6937-5677
Claudia HöbartnerInstitute of Organic Chemistry and Center for Nanosystems Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.ORCID https://orcid.org/0000-0002-4548-2299
Yimin HuDepartment of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.ORCID https://orcid.org/0000-0002-6965-8965
Shekhar JadhavEuropean Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.ORCID https://orcid.org/0009-0009-4682-7568
Philip E JohnsonDepartment of Chemistry, York University, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0002-5573-4891
Christopher P JonesBiochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.ORCID https://orcid.org/0000-0001-7780-5278
Deepak KoiralaDepartment of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, USA.ORCID https://orcid.org/0000-0001-6424-3173
Emil L KristoffersenDepartment of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.ORCID https://orcid.org/0000-0001-8965-8201
Eric LargyUniversity of Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA, Bordeaux, France.ORCID https://orcid.org/0000-0002-6140-9788
Anna LewickaDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.ORCID https://orcid.org/0000-0002-9578-2628
Cameron D MackerethUniversity of Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA, Bordeaux, France.ORCID https://orcid.org/0000-0002-0776-7947
Marco MarciaEuropean Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.ORCID https://orcid.org/0000-0003-2430-0713
Michela NigroEuropean Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.ORCID https://orcid.org/0000-0003-1847-475X
Manju OjhaDepartment of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, USA.ORCID https://orcid.org/0009-0001-3907-431X
Joseph A PiccirilliDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.ORCID https://orcid.org/0000-0002-0541-6270
Phoebe A RiceDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.ORCID https://orcid.org/0000-0002-3467-341X
Heewhan ShinDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.ORCID https://orcid.org/0000-0001-9656-6639
Anna-Lena SteckelbergDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.ORCID https://orcid.org/0000-0001-7988-9946
Zhaoming SuThe State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.ORCID https://orcid.org/0000-0002-9279-1721
Yoshita SrivastavaDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.ORCID https://orcid.org/0000-0001-9091-9851
Liu WangThe State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.ORCID https://orcid.org/0000-0003-1243-9654
Yuan WuHoward Hughes Medical Institute, Stanford University, Stanford, California, USA.ORCID https://orcid.org/0009-0000-6122-2457
Jiahao XieMingle Scope (Chengdu), Chengdu, China.ORCID https://orcid.org/0000-0002-4632-2959
Nikolaj H ZwergiusInterdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.ORCID https://orcid.org/0009-0007-4155-2468
John MoultDepartment of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA.ORCID https://orcid.org/0000-0002-3012-2282
Andriy KryshtafovychGenome Center, University of California, Davis, California, USA.ORCID https://orcid.org/0000-0001-5066-7178
Funding
The Stanford-SLAC CryoEM Center supplementU24GM129541 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH, HEDMAN, BRITT · 2018 to 2023
$54.8MUser Training and OutreachP30GM124165 · NIGMS · CORNELL UNIVERSITY · PI STEVEN E EALICK · 2018 to 2026
$34.2MCenter for Structural Biology of HIV RNAU54AI170660 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALICE TELESNITSKY · 2022 to 2026
$32.1MUnified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MProspective analysis to determine model accuracy performance and boundaries in the post-AlphaFold2 environmentR01GM100482 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI FIDELIS, KRZYSZTOF A · 2012 to 2025
$11.1MNext-generation computational/chemical methods for complex RNA structuresR35GM122579 · NIGMS · STANFORD UNIVERSITY · PI Rhiju Das · 2017 to 2026
$7.2MGraduate Training at The Chemistry Biology InterfaceT32GM066706 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE COUNTY · PI SELEY-RADTKE, KATHERINE L, SMITH, AARON T · 2004 to 2023
$3.3MStructure and Function of Non-Coding RNAR35GM149336 · NIGMS · UNIVERSITY OF CHICAGO · PI Joseph Anthony Piccirilli · 2023 to 2026
$2.8MPixel Array Detector for Macromolecular CrystallographyS10OD021527 · OD · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2016 to 2016
$2.0MUnderstanding the antiviral roles of acellular RNA quality control pathwayR35GM150778 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Anna-Lena Steckelberg · 2023 to 2026
$1.6MAarhus UniversityBio-X Bowes Graduate Student FellowshipCenter for Structural Biology of HIV-1 RNA (CRNA) Collaborative Development Pilot Grant Program NIAID1U54AI170660Deutsche Forschungsgemeinschaft 463143961EMBION Cryo-EM Facility at iNANOEuropean Commission (HORIZON-MSCA-2023-DN-01) 101168667France Canada Research FundGottfried Wilhelm Leibniz ProgrammeHoward Hughes Medical InstituteNational Institutes of Health Common Fund Transformative High-Resolution Cryo-Electron Microscopy Program U24GM129541National Key Research and Development Program of ChinaNational Natural Science Foundation of ChinaNational Science Foundation 2330652National Science Foundation GRFP DGE-2036197Natural Science Foundation of China 32222040Natural Sciences and Engineering Research Council of CanadaNIAID NIH HHS U54 AI170660NIGMS NIH HHS P30 GM124165NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM100482NIGMS NIH HHS R35 GM122579NIGMS NIH HHS R35 GM149336NIGMS NIH HHS R35 GM150778NIGMS NIH HHS T32 GM066706NIGMS NIH HHS U24 GM129541NIH HHS GM066706NIH HHS K22HL139920-01NIH HHS R01GM079429NIH HHS R35GM122579NIH HHS R35GM150778NIH HHS S10 OD021527NIH/NIGMS R01GM100482NIH/NIGMS R35GM149336NIH-ORIP HEINovo Nordisk FoundationStanford Bio-XSwedish National Research Council 2024-04107U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory 10.13039/100000015Villum Foundation
Abstract
Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
Indexed as
Computational BiologyNucleic AcidsRNAAlgorithmsHydrogen BondingLigandsModels, MolecularNucleic Acid ConformationProteinsLigandsNucleic AcidsProteinsRNACASPcommunity‐wide experimentfunctionally relevant structure prediction accuracynucleic‐acid‐protein complexesnucleic acid structure predictionRNA folding
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.