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Automated 3D structure composition for large RNAs

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.21806openalex-snapshot

Automated RNA tertiary structure prediction from secondary structure and low‐resolution restraints

inferredcites →https://doi.org/10.1006/jmbi.1997.1284openalex-snapshot

Torsion angle dynamics for NMR structure calculation with the new program Dyana

inferredcites →https://doi.org/10.1006/jmbi.2001.4626openalex-snapshot

Quantitative analysis of nucleic acid three-dimensional structures

inferredcites →https://doi.org/10.1007/978-0-387-72774-5openalex-snapshot

Machine Translation: Its Scope and Limits

inferredcites →https://doi.org/10.1007/978-3-642-25740-7openalex-snapshot

RNA 3D Structure Analysis and Prediction

inferredcites →https://doi.org/10.1007/bf00818163openalex-snapshot

Fast folding and comparison of RNA secondary structures

inferredcites →https://doi.org/10.1016/0005-2795(75)90109-9openalex-snapshot

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

inferredcites →https://doi.org/10.1016/j.sbi.2006.05.010openalex-snapshot

Prediction of RNA secondary structure by free energy minimization

inferredcites →https://doi.org/10.1016/j.sbi.2009.12.001openalex-snapshot

Structural insights into RNA interference

inferredcites →https://doi.org/10.1016/s0006-3495(92)81649-1openalex-snapshot

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

inferredcites →https://doi.org/10.1016/s1090-7807(02)00014-9openalex-snapshot

The Xplor-NIH NMR molecular structure determination package

inferredcites →https://doi.org/10.1021/bk-1998-0682openalex-snapshot

Molecular Modeling of Nucleic Acids

inferredcites →https://doi.org/10.1021/bk-1998-0682.ch024openalex-snapshot

Modeling Unusual Nucleic Acid Structures

inferredcites →https://doi.org/10.1021/ja043822vopenalex-snapshot

RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)

inferredcites →https://doi.org/10.1038/nature06684openalex-snapshot

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

inferredcites →https://doi.org/10.1038/nmeth.1433openalex-snapshot

Atomic accuracy in predicting and designing noncanonical RNA structure

inferredcites →https://doi.org/10.1038/nprot.2006.249openalex-snapshot

Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

inferredcites →https://doi.org/10.1073/pnas.0401799101openalex-snapshot

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

inferredcites →https://doi.org/10.1073/pnas.0806929106openalex-snapshot

Accurate SHAPE-directed RNA structure determination

inferredcites →https://doi.org/10.1074/jbc.m110.182840openalex-snapshot

The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function

inferredcites →https://doi.org/10.1080/07391102.2008.10531240openalex-snapshot

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

inferredcites →https://doi.org/10.1093/bioinformatics/btn328openalex-snapshot

iFoldRNA: three-dimensional RNA structure prediction and folding

inferredcites →https://doi.org/10.1093/bioinformatics/btp252openalex-snapshot

PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

inferredcites →https://doi.org/10.1093/bioinformatics/btp576openalex-snapshot

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

inferredcites →https://doi.org/10.1093/bioinformatics/btq321openalex-snapshot

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

inferredcites →https://doi.org/10.1093/nar/gkg365openalex-snapshot

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

inferredcites →https://doi.org/10.1093/nar/gkg529openalex-snapshot

Tools for the automatic identification and classification of RNA base pairs

inferredcites →https://doi.org/10.1093/nar/gkm216openalex-snapshot

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

inferredcites →https://doi.org/10.1093/nar/gkm786openalex-snapshot

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

inferredcites →https://doi.org/10.1093/nar/gkq1021openalex-snapshot

The RCSB Protein Data Bank: redesigned web site and web services

inferredcites →https://doi.org/10.1093/nar/gkq1320openalex-snapshot

ModeRNA: a tool for comparative modeling of RNA 3D structure

inferredcites →https://doi.org/10.1093/nar/gkr1081openalex-snapshot

Statistical evaluation of improvement in RNA secondary structure prediction

inferredcites →https://doi.org/10.1093/nar/gkr385openalex-snapshot

The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

inferredcites →https://doi.org/10.1093/nar/gkr773openalex-snapshot

Simplified RNA secondary structure mapping by automation of SHAPE data analysis

inferredcites →https://doi.org/10.1093/nass/nrl033openalex-snapshot

High-throughput method for the prediction of low-resolution, three-dimensional RNA structures

inferredcites →https://doi.org/10.1107/s0567739476001873openalex-snapshot

A solution for the best rotation to relate two sets of vectors

inferredcites →https://doi.org/10.1109/tcbb.2010.104openalex-snapshot

Fast Flexible Modeling of RNA Structure Using Internal Coordinates

inferredcites →https://doi.org/10.1186/1471-2105-11-129openalex-snapshot

RNAstructure: software for RNA secondary structure prediction and analysis

inferredcites →https://doi.org/10.1186/1471-2105-11-231openalex-snapshot

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

inferredcites →https://doi.org/10.1186/1476-4598-9-134openalex-snapshot

Microprocessor of microRNAs: regulation and potential for therapeutic intervention

inferredcites →https://doi.org/10.1261/rna.1270809openalex-snapshot

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

inferredcites →https://doi.org/10.1261/rna.1700409openalex-snapshot

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

inferredcites →https://doi.org/10.1261/rna.2112110openalex-snapshot

Turning limited experimental information into 3D models of RNA

inferredcites →https://doi.org/10.1261/rna.7214405openalex-snapshot

SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

inferredcites →https://doi.org/10.1371/journal.pbio.0060096openalex-snapshot

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

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In silico designed RNA aptamer against epithelial cell adhesion molecule for cancer cell imaging

inferred← citeshttps://doi.org/10.1016/j.bbrc.2024.150581openalex-snapshot

Toll-like receptor 21 in Labeo rohita recognizes double-stranded RNA and lipopolysaccharides by engaging the critical motifs in the LRR domain and gets activated against bacterial assaults

inferred← citeshttps://doi.org/10.1016/j.bcmd.2015.07.009openalex-snapshot

APOBEC3G governs to ensure cellular oncogenic transformation

inferred← citeshttps://doi.org/10.1016/j.biochi.2013.07.034openalex-snapshot

Biological evidence for the world's smallest tRNAs

inferred← citeshttps://doi.org/10.1016/j.biochi.2015.03.013openalex-snapshot

The 55S mammalian mitochondrial ribosome and its tRNA-exit region

inferred← citeshttps://doi.org/10.1016/j.biochi.2018.09.005openalex-snapshot

Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques

inferred← citeshttps://doi.org/10.1016/j.biochi.2020.07.019openalex-snapshot

The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data

inferred← citeshttps://doi.org/10.1016/j.biochi.2020.10.005openalex-snapshot

In silico molecular docking in DNA aptamer development

inferred← citeshttps://doi.org/10.1016/j.biochi.2024.12.011openalex-snapshot

The neutralisation and inhibitory effects of new tRNA-mimetic aptamer against cytotoxin-induced cytotoxicity in human skin keratinocytes

inferred← citeshttps://doi.org/10.1016/j.bios.2022.114257openalex-snapshot

Multifunctional biosensor constructed by Ag-coating magnetic-assisted unique urchin core porous shell structure for dual SERS enhancement, enrichment, and quantitative detection of multi-components inflammatory markers

inferred← citeshttps://doi.org/10.1016/j.bios.2022.114887openalex-snapshot

High content design of riboswitch biosensors: All-around rational module-by-module design

inferred← citeshttps://doi.org/10.1016/j.bpc.2020.106492openalex-snapshot

The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application

inferred← citeshttps://doi.org/10.1016/j.bpc.2024.107259openalex-snapshot

Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice

inferred← citeshttps://doi.org/10.1016/j.bpc.2024.107308openalex-snapshot

In silico analysis of aptamer-RNA conjugate interactions with human transferrin receptor

inferred← citeshttps://doi.org/10.1016/j.bpj.2014.12.014openalex-snapshot

Structural Analysis of Adenovirus VAI RNA Defines the Mechanism of Inhibition of PKR

inferred← citeshttps://doi.org/10.1016/j.bpj.2015.11.006openalex-snapshot

Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

inferred← citeshttps://doi.org/10.1016/j.bpj.2018.08.030openalex-snapshot

Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions

inferred← citeshttps://doi.org/10.1016/j.bpj.2020.10.012openalex-snapshot

Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element

inferred← citeshttps://doi.org/10.1016/j.bpj.2021.11.016openalex-snapshot

rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

inferred← citeshttps://doi.org/10.1016/j.bpj.2022.04.027openalex-snapshot

Unraveling the binding mode of a methamphetamine aptamer: A spectroscopic and calorimetric study

inferred← citeshttps://doi.org/10.1016/j.bpj.2022.08.017openalex-snapshot

FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures

inferred← citeshttps://doi.org/10.1016/j.bpj.2022.11.2396openalex-snapshot

Predicting 3D RNA structure from solely the nucleotide sequence using Euclidean distance neural networks

inferred← citeshttps://doi.org/10.1016/j.bpj.2023.03.017openalex-snapshot

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

inferred← citeshttps://doi.org/10.1016/j.bpj.2023.10.011openalex-snapshot

Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks

inferred← citeshttps://doi.org/10.1016/j.bpj.2024.01.026openalex-snapshot

Machine learning in RNA structure prediction: Advances and challenges

inferred← citeshttps://doi.org/10.1016/j.bpj.2024.02.018openalex-snapshot

3dDNAscoreA: A scoring function for evaluation of DNA 3D structures

inferred← citeshttps://doi.org/10.1016/j.bpj.2025.07.013openalex-snapshot

rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation

inferred← citeshttps://doi.org/10.1016/j.bpj.2026.04.003openalex-snapshot

TriRNASP: A knowledge-based potential with three-body effects for accurate RNA structure evaluation

inferred← citeshttps://doi.org/10.1016/j.cbpa.2024.102479openalex-snapshot

RNA nanotechnology on the horizon: Self-assembly, chemical modifications, and functional applications

inferred← citeshttps://doi.org/10.1016/j.cclet.2016.10.029openalex-snapshot

Discovery of novel double pyrazole Schiff base derivatives as anti-tobacco mosaic virus (TMV) agents

inferred← citeshttps://doi.org/10.1016/j.cej.2024.158746openalex-snapshot

Capture and detection of nucleic acid aptamer target proteins in colorectal cancer

inferred← citeshttps://doi.org/10.1016/j.cell.2018.04.038openalex-snapshot

Structure of Telomerase with Telomeric DNA

inferred← citeshttps://doi.org/10.1016/j.cell.2022.12.016openalex-snapshot

Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin

inferred← citeshttps://doi.org/10.1016/j.celrep.2018.12.054openalex-snapshot

Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires

inferred← citeshttps://doi.org/10.1016/j.celrep.2021.108914openalex-snapshot

Asterix/Gtsf1 Links tRNAs and piRNA Silencing of Retrotransposons

inferred← citeshttps://doi.org/10.1016/j.chempr.2018.09.015openalex-snapshot

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

inferred← citeshttps://doi.org/10.1016/j.chempr.2021.05.021openalex-snapshot

Computer-aided design of RNA-targeted small molecules: A growing need in drug discovery

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2019.107088openalex-snapshot

DM-RPIs: Predicting ncRNA-protein interactions using stacked ensembling strategy

inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.105502openalex-snapshot

Unveiling the nature's fruit basket to computationally identify Citrus sinensis csi-mir169–3p as a probable plant miRNA against Reference and Omicron SARS-CoV-2 genome

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.08.017openalex-snapshot

3dRNA: Building RNA 3D structure with improved template library

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.08.024openalex-snapshot

Two alternative conformations of mRNA in the human ribosome during elongation and termination of translation as revealed by EPR spectroscopy

inferred← citeshttps://doi.org/10.1016/j.csbj.2022.11.036openalex-snapshot

Consequences of genetic variants in miRNA genes

inferred← citeshttps://doi.org/10.1016/j.csbj.2023.04.028openalex-snapshot

Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques

inferred← citeshttps://doi.org/10.1016/j.csbj.2025.03.021openalex-snapshot

Transformers in RNA structure prediction: A review

inferred← citeshttps://doi.org/10.1016/j.csbj.2025.08.037openalex-snapshot

Semi-supervised segmentation of RNA 3D structures using density-based clustering

inferred← citeshttps://doi.org/10.1016/j.csbj.2025.12.010openalex-snapshot

Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution

inferred← citeshttps://doi.org/10.1016/j.dam.2014.04.010openalex-snapshot

Optimal pathway reconstruction on 3D NMR maps

inferred← citeshttps://doi.org/10.1016/j.drup.2024.101097openalex-snapshot

CircPDIA3/miR-449a/XBP1 feedback loop curbs pyroptosis by inhibiting palmitoylation of the GSDME-C domain to induce chemoresistance of colorectal cancer

inferred← citeshttps://doi.org/10.1016/j.drup.2024.101126openalex-snapshot

crVDAC3 alleviates ferroptosis by impeding HSPB1 ubiquitination and confers trastuzumab deruxtecan resistance in HER2-low breast cancer

inferred← citeshttps://doi.org/10.1016/j.drup.2026.101475openalex-snapshot

Nucleolin shields PTBP1 from autophagic degradation to sustain gemcitabine resistance in bladder cancer

inferred← citeshttps://doi.org/10.1016/j.exer.2020.108277openalex-snapshot

In silico model of mtDNA mutations effect on secondary and 3D structure of mitochondrial rRNA and tRNA in Leber’s hereditary optic neuropathy

inferred← citeshttps://doi.org/10.1016/j.gendis.2022.07.002openalex-snapshot

Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

inferred← citeshttps://doi.org/10.1016/j.hal.2019.101642openalex-snapshot

Importance of messenger RNA stability of toxin synthetase genes for monitoring toxic cyanobacterial bloom

inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e38234openalex-snapshot

Development and characterization of high-affinity aptamers for HIV protease detection

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.126412openalex-snapshot

Mechanisms of ssDNA aptamer binding to Cd2+ in aqueous solution: A molecular dynamics study

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.147772openalex-snapshot

CircPRUNE inhibits the proliferation and metastasis of oral squamous cell carcinoma through PTBP3/NOTCH3 signaling axis

inferred← citeshttps://doi.org/10.1016/j.imu.2020.100471openalex-snapshot

Exploring novel therapeutic strategies against vivax malaria through an integrated computational investigation to inhibit the merozoite surface protein−1 of Plasmodium vivax

inferred← citeshttps://doi.org/10.1016/j.imu.2021.100670openalex-snapshot

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1

inferred← citeshttps://doi.org/10.1016/j.isci.2019.05.019openalex-snapshot

Evolution of Subgenomic RNA Shapes Dengue Virus Adaptation and Epidemiological Fitness

inferred← citeshttps://doi.org/10.1016/j.isci.2025.113299openalex-snapshot

SELEX identifies high-affinity RNA targets for chromatin-binding proteins PARP1 and MeCP2

inferred← citeshttps://doi.org/10.1016/j.isci.2026.117803openalex-snapshot

Diversification and hybridization within the Spirochona gemmipara complex driven by gammarid host range shifts

inferred← citeshttps://doi.org/10.1016/j.jbc.2021.100555openalex-snapshot

An RNA-centric historical narrative around the Protein Data Bank

inferred← citeshttps://doi.org/10.1016/j.jbc.2024.108015openalex-snapshot

mRNA vaccine sequence and structure design and optimization: Advances and challenges

inferred← citeshttps://doi.org/10.1016/j.jbc.2025.110522openalex-snapshot

Molecular basis of the autoregulatory mechanism of motor neuron-related splicing factor 30

inferred← citeshttps://doi.org/10.1016/j.jbc.2026.113264openalex-snapshot

Intragenomic riboregulatory interaction modulates the conformation of the hepatitis C virus 3′X RNA

inferred← citeshttps://doi.org/10.1016/j.jconrel.2025.114031openalex-snapshot

Targeted delivery of therapeutics to metastatic lung cancer cells using aptamer-conjugated nanoemulsions

inferred← citeshttps://doi.org/10.1016/j.jece.2026.122276openalex-snapshot

Harnessing aptamers for theranostic applications against multidrug-resistant bacteria: Current trends, bottlenecks and environmental relevance

inferred← citeshttps://doi.org/10.1016/j.jes.2025.12.055openalex-snapshot

WTAP upregulates HK2 expression via m6A methylation to reprogram cell glycolysis and stemness under Cr(VI) exposure

inferred← citeshttps://doi.org/10.1016/j.jhazmat.2021.127939openalex-snapshot

Development of novel fluorescence-based and label-free noncanonical G4-quadruplex-like DNA biosensor for facile, specific, and ultrasensitive detection of fipronil

inferred← citeshttps://doi.org/10.1016/j.jid.2022.08.034openalex-snapshot

miRNA-203b-3p Induces Acute and Chronic Pruritus through 5-HTR2B and TRPV4

inferred← citeshttps://doi.org/10.1016/j.jmb.2014.11.013openalex-snapshot

A Novel Open-Barrel Structure of Octameric Translin Reveals a Potential RNA Entryway

inferred← citeshttps://doi.org/10.1016/j.jmb.2015.11.011openalex-snapshot

Progress and Current Challenges in Modeling Large RNAs

inferred← citeshttps://doi.org/10.1016/j.jmb.2017.09.017openalex-snapshot

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly

inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167452openalex-snapshot

3dRNA: 3D Structure Prediction from Linear to Circular RNAs

inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.04.012openalex-snapshot

Effect of PDGF-B aptamer on PDGFRβ/PDGF-B interaction: Molecular dynamics study

inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107872openalex-snapshot

In silico approach for Post-SELEX DNA aptamers: A mini-review

inferred← citeshttps://doi.org/10.1016/j.jmgm.2024.108839openalex-snapshot

Structure based computational RNA design towards MafA transcriptional repressor implicated in multiple myeloma

inferred← citeshttps://doi.org/10.1016/j.jmgm.2025.109071openalex-snapshot

Elucidating OASL-RNA Interactions: Structural and energetic insights into vault RNAs binding

inferred← citeshttps://doi.org/10.1016/j.jsb.2019.06.002openalex-snapshot

VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures

inferred← citeshttps://doi.org/10.1016/j.jtbi.2020.110268openalex-snapshot

Computational predictive approaches for interaction and structure of aptamers

inferred← citeshttps://doi.org/10.1016/j.lfs.2025.123927openalex-snapshot

MLN4924, neddylation inhibitor suppresses hypoxia induced retinal angiogenesis by targeting Human Antigen R signaling

inferred← citeshttps://doi.org/10.1016/j.mattod.2025.06.020openalex-snapshot

Aptamers in drug delivery development

inferred← citeshttps://doi.org/10.1016/j.mbs.2025.109485openalex-snapshot

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

inferred← citeshttps://doi.org/10.1016/j.microc.2024.110829openalex-snapshot

Highly-efficient selection of interferon gamma-specific aptamers and development of a sensitive fiber-optic evanescent wave aptasensor

inferred← citeshttps://doi.org/10.1016/j.microc.2024.112007openalex-snapshot

MNPs-aptazymes-PtNPs molecular motor biosensor mediated by circular cleavage reactions for the ultrasensitive detection of aflatoxin B1 in real samples

inferred← citeshttps://doi.org/10.1016/j.microc.2025.115414openalex-snapshot

When simulations meet reality: a critical analysis of conformational accuracy in DNA aptamer-target interactions

inferred← citeshttps://doi.org/10.1016/j.microc.2026.119652openalex-snapshot

Improved whole-bacteria SELEX for specific aptamer screening of Burkholderia gladioli pv. cocovenenans: target identification and binding mechanism

inferred← citeshttps://doi.org/10.1016/j.molbiopara.2017.08.006openalex-snapshot

Structural and evolutionary analysis of Leishmania Alba proteins

inferred← citeshttps://doi.org/10.1016/j.molcel.2020.10.028openalex-snapshot

Functional Atlas of Primary miRNA Maturation by the Microprocessor

inferred← citeshttps://doi.org/10.1016/j.molcel.2021.02.021openalex-snapshot

Structural basis for conformational equilibrium of the catalytic spliceosome

inferred← citeshttps://doi.org/10.1016/j.molcel.2022.09.020openalex-snapshot

Structural insights into RNA-mediated transcription regulation in bacteria

inferred← citeshttps://doi.org/10.1016/j.molcel.2022.10.010openalex-snapshot

Structural and functional basis of mammalian microRNA biogenesis by Dicer

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