Physics-based de novo prediction of RNA 3D structures.

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Journal of Physical Chemistry B

• Publication date

  2011-04-14

• Fields of study

  Medicine, Physics, Computer Science

• Identifiers
  DOI 10.1021/jp112059yPMID 21413701PMCID PMC3072456
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Predicting loop-helix tertiary structural contacts in RNA pseudoknots.

  2010cited by this paper
• On the significance of an RNA tertiary structure prediction.

  2010cited by this paper
• Turning limited experimental information into 3D models of RNA.

  2010cited by this paper
• HiRE-RNA: a high resolution coarse-grained energy model for RNA.

  2010cited by this paper
• Improved free energy parameters for RNA pseudoknotted secondary structure prediction.

  2010cited by this paper
• Computational approaches to 3D modeling of RNA

  2010cited by this paper
• Coarse-grained model for simulation of RNA three-dimensional structures.

  2010cited by this paper
• DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model

  2010cited by this paper
• Atomic accuracy in predicting and designing non-canonical RNA structure

  2010cited by this paper
• Computing the conformational entropy for RNA folds.

  2010cited by this paper
• RNA structure determination using SAXS data.

  2010cited by this paper
• Comparison and functional implications of the 3D architectures of viral tRNA-like structures.

  2009cited by this paper
• Toward a structural understanding of IRES RNA function.

  2009cited by this paper
• Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

  2009cited by this paper
• New metrics for comparing and assessing discrepancies between RNA 3D structures and models.

  2009cited by this paper
• Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

  2009cited by this paper
• MicroRNAs: Target Recognition and Regulatory Functions

  2009cited by this paper
• Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation.

  2009cited by this paper
• Analysis of four-way junctions in RNA structures.

  2009cited by this paper
• Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

  2009cited by this paper
• Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics.

  2009cited by this paper
• Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.

  2009cited by this paper
• Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.

  2008cited by this paper
• Structural inference of native and partially folded RNA by high-throughput contact mapping

  2008cited by this paper
• A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

  2008cited by this paper
• iFoldRNA: three-dimensional RNA structure prediction and folding

  2008cited by this paper
• Structural Elements in RNA

  2008cited by this paper
• Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme

  2008cited by this paper
• The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

  2008cited by this paper
• Frameshifting RNA pseudoknots: Structure and mechanism

  2008cited by this paper
• Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

  2008cited by this paper
• Kinetic barriers and the role of topology in protein and RNA folding

  2008cited by this paper
• RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

  2008cited by this paper
• RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

  2008cited by this paper
• Predicting helical coaxial stacking in RNA multibranch loops.

  2007cited by this paper
• The role of site accessibility in microRNA target recognition

  2007cited by this paper
• Bridging the gap in RNA structure prediction.

  2007cited by this paper
• The biophysics of RNA.

  2007cited by this paper
• Automated de novo prediction of native-like RNA tertiary structures

  2007cited by this paper
• Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies.

  2006cited by this paper
• Structure of human tryptophanyl-tRNA synthetase in complex with tRNATrp reveals the molecular basis of tRNA recognition and specificity

  2006cited by this paper
• Structure and function of telomerase RNA.

  2006cited by this paper
• NMR Structure of the Full-length Linear Dimer of Stem-Loop-1 RNA in the HIV-1 Dimer Initiation Site*♦

  2006cited by this paper
• YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

  2006cited by this paper
• Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2

  2006cited by this paper
• Prediction of RNA secondary structure by free energy minimization.

  2006cited by this paper
• Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.

  2006cited by this paper
• Predicting RNA pseudoknot folding thermodynamics

  2006cited by this paper
• Towards understanding the catalytic core structure of the spliceosome.

  2005cited by this paper
• Secondary structure prediction of interacting RNA molecules.

  2005cited by this paper
• Dimerization of retroviral RNA genomes: an inseparable pair

  2004cited by this paper
• U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

  2004cited by this paper
• NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus.

  2004cited by this paper
• Simulation and modeling of nucleic acid structure, dynamics and interactions.

  2004cited by this paper
• Vienna RNA secondary structure server

  2003cited by this paper
• Refined solution structure of the iron-responsive element RNA using residual dipolar couplings.

  2003cited by this paper
• A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme.

  2003cited by this paper
• Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis

  2001cited by this paper
• Geometric nomenclature and classification of RNA base pairs.

  2001cited by this paper
• The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

  2000cited by this paper
• tRNA aminoacylation by arginyl‐tRNA synthetase: induced conformations during substrates binding

  2000cited by this paper
• Thermodynamics of single mismatches in RNA duplexes.

  1999cited by this paper
• Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

  1999cited by this paper
• Modeling Unusual Nucleic Acid Structures

  1998cited by this paper
• Stepping through an RNA structure: A novel approach to conformational analysis.

  1998cited by this paper
• RNA folding causes secondary structure rearrangement.

  1998cited by this paper
• NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.

  1998cited by this paper
• The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution

  1997cited by this paper
• Predicting thermodynamic properties of RNA.

  1995cited by this paper
• A second generation force field for the simulation of proteins

  1995cited by this paper
• Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome.

  1994cited by this paper
• A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome.

  1992cited by this paper
• Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.

  1990cited by this paper
• Improved predictions of secondary structures for RNA.

  1989cited by this paper
• On finding all suboptimal foldings of an RNA molecule.

  1989cited by this paper
• Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.

  1987cited by this paper
• Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25.

  1982cited by this paper
• Configurational Statistics of Polynucleotide Chains. An Updated Virtual Bond Model to Treat Effects of Base Stacking

  1980cited by this paper
• Fast algorithm for predicting the secondary structure of single-stranded RNA.

  1980cited by this paper
• A different best rigid-body molecular fit routine

  1977cited by this paper
• Optimised parameters for RNA double-helices.

  1972cited by this paper
• Statistical mechanics of chain molecules

  1970cited by this paper
• Open access, freely available online Primer Pseudoknots: RNA Structures with Diverse Functions

  year unknowncited by this paper

• TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction

  2026cites this paper
• Computational approaches for RNA structure prediction and design.

  2026cites this paper
• ATLAS: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions

  2026cites this paper
• Has AlphaFold3 achieved success for RNA?

  2025cites this paper
• Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes

  2025influential citation
• Aptamers Meet Structural Bioinformatics, Computational Chemistry, and Artificial Intelligence

  2025cites this paper
• Selection and validation of a cell-internalizing DNA aptamer targeting esophageal squamous cell carcinoma.

  2025cites this paper
• Learning RNA language through pre-trained models: From sequence to structure

  2025cites this paper
• Cross-talk between RNA secondary and three-dimensional structure prediction: a comprehensive study

  2025influential citation
• GARN3: A coarse-grained helix centered technique for RNA 3D structures prediction

  2025cites this paper
• rsRNASP1: a distance and dihedral dependent statistical potential for RNA 3D structure evaluation.

  2025cites this paper
• Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.

  2025cites this paper
• Advances in RNA contact prediction: a benchmark evaluation of computational methods

  2025cites this paper
• Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions

  2025cites this paper
• Consolidate Overview of Ribonucleic Acid Molecular Dynamics: From Molecular Movements to Material Innovations

  2025cites this paper
• RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation

  2025cites this paper
• Aptamer biosensor design for the detection of endocrine-disrupting chemicals small organic molecules using novel bioinformatics methods.

  2024cites this paper
• State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction

  2024cites this paper
• Machine Learning in RNA Structure Prediction: Advances and Challenges.

  2024cites this paper
• Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction

  2024cites this paper
• RNA-Puzzles Round V: blind predictions of 23 RNA structures

  2024cites this paper
• smFRET-assisted RNA structure prediction

  2024cites this paper
• Entropy‐Driven Self‐Assembly of DNA Origami Isomers

  2024cites this paper
• Prediction of aptamer affinity using an artificial intelligence approach.

  2024cites this paper
• Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions

  2024cites this paper
• Has AlphaFold 3 reached its success for RNAs?

  2024cites this paper
• ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures

  2024cites this paper
• RNA Folding Based on 5 Beads Model and Multiscale Simulation

  2023cites this paper
• Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.

  2023cites this paper
• Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15

  2023cites this paper
• Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.

  2023cites this paper
• Terahertz waves regulate the mechanical unfolding of tau pre-mRNA hairpins

  2023cites this paper
• Advancements in small molecule drug design: A structural perspective.

  2023cites this paper
• RNA origami: design, simulation and application

  2023cites this paper
• RNA 3D Structure Prediction: Progress and Perspective

  2023influential citation
• Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein

  2023cites this paper
• Using 3dRNA/DNA for RNA and DNA 3D Structure Prediction and Evaluation

  2023cites this paper
• Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.

  2023cites this paper
• RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling

  2023cites this paper
• FebRNA: an automated fragment-ensemble-based model for building RNA 3D structures

  2022cites this paper
• RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures

  2022cites this paper
• 3dRNA: 3D Structure Prediction from Linear to Circular RNAs.

  2022cites this paper
• Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction

  2022cites this paper
• Advances in RNA 3D Structure Prediction

  2022cites this paper
• Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction

  2022cites this paper
• Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation.

  2022cites this paper
• Computational tools to study RNA-protein complexes

  2022cites this paper
• 3dDNA: A Computational Method of Building DNA 3D Structures

  2022cites this paper
• Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences

  2022cites this paper
• Predicting 3D RNA structure from solely the nucleotide sequence using Euclidean distance neural networks

  2022cites this paper
• cgRNASP-CN: a minimal coarse-grained representation-based statistical potential for RNA 3D structure evaluation

  2022cites this paper
• cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation

  2022cites this paper
• Statistical potentials for 3D structure evaluation: From proteins to RNAs*

  2021cites this paper
• An Integrated Tool for RNA 3D Structure Prediction and Analysis

  2021cites this paper
• rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

  2021cites this paper
• Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential.

  2021cites this paper
• Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.

  2021cites this paper
• umFold: An Algorithm to Predict RNA Tertiary

  2021cites this paper
• RNA 3D Structure Prediction Using Coarse-Grained Models

  2021cites this paper
• Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.

  2021cites this paper
• Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.

  2021cites this paper
• Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

  2021cites this paper
• A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field

  2021cites this paper
• IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures.

  2021influential citation
• Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction

  2020cites this paper
• siRNA Design to Silence the 3′UTR Region of Zika Virus

  2020cites this paper
• Prediction of RNA secondary structure with pseudoknots using coupled deep neural networks

  2020cites this paper
• 3dRNA: Building RNA 3D structure with improved template library

  2020cites this paper
• The Multiscale Future of RNA Modeling

  2020cites this paper
• Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.

  2020cites this paper
• Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase

  2020cites this paper
• Computational predictive approaches for interaction and structure of aptamers.

  2020cites this paper
• Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

  2019cites this paper
• Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

  2019cites this paper
• Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations

  2019cites this paper
• What is the best reference state for building statistical potentials in RNA 3D structure evaluation?

  2019cites this paper
• 3D structure stability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study.

  2019cites this paper
• VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.

  2019influential citation
• Limits in accuracy and a strategy of RNA structure prediction using experimental information

  2019cites this paper
• Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

  2019influential citation
• 3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction

  2019cites this paper
• RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks

  2018cites this paper
• IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.

  2018cites this paper
• RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

  2018cites this paper
• Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

  2018cites this paper
• Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

  2018cites this paper
• Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.

  2018cites this paper
• Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

  2018cites this paper
• Predicting Cotranscriptional Folding Kinetics For Riboswitch.

  2018cites this paper
• Modeling structure, stability and flexibility of double-stranded RNAs in salt solutions

  2018cites this paper
• Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: promoter and aptamer designs

  2018cites this paper
• Evaluation of RNA secondary structure prediction for both base-pairing and topology

  2018cites this paper
• RNA Biology: Methods and Techniques

  2018cites this paper
• Kajian Prediksi 3-Dimensi Biomarker Kanker Payudara Dari Jalur Ekspresi LincRNA-ROR/MIR-145/ARF6 [3D Prediction of Breast Cancer Biomarker from The Expression Pathway of LincRNA-ROR/MIR-145/ARF6]

  2018cites this paper
• Information Transfer and Dynamics of Nucleic Acids studied by Theoretical Approaches

  2018cites this paper
• A novel knowledge-based potential for RNA 3D structure evaluation

  2018cites this paper
• DỰ ĐOÁN CẤU TRÚC BẬC HAI RNA BẰNG SỰ KẾT HỢP THUẬT TOÁN DI TRUYỀN VÀ LOGIC MỜ

  2018cites this paper
• RNA structure prediction: from 2D to 3D.

  2017cites this paper
• Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation

  2017influential citation
• A New Method to Predict Ion Effects in RNA Folding.

  2017cites this paper