| scholarly article | Q13442814 |
| P818 | arXiv ID | 1905.07680 |
| P8978 | DBLP publication ID | journals/ploscb/ShiJFTT18 |
| P356 | DOI | 10.1371/JOURNAL.PCBI.1006222 |
| P932 | PMC publication ID | 6007934 |
| P698 | PubMed publication ID | 29879103 |
| P50 | author | Zhi-Jie Tan | Q89025260 |
| P2093 | author name string | Lei Jin | |
| Ya-Lan Tan | |||
| Ya-Zhou Shi | |||
| Chen-Jie Feng | |||
| P2860 | cites work | Pseudoknots: RNA structures with diverse functions | Q21092809 |
| Mfold web server for nucleic acid folding and hybridization prediction | Q24498105 | ||
| The Protein Data Bank | Q24515306 | ||
| Automated 3D structure composition for large RNAs | Q24622388 | ||
| Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters | Q24647503 | ||
| Salt dependence of nucleic acid hairpin stability | Q24650345 | ||
| Frameshifting RNA pseudoknots: structure and mechanism | Q24657279 | ||
| Automated de novo prediction of native-like RNA tertiary structures | Q24673712 | ||
| Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot | Q27617509 | ||
| Characterization of the mechanical unfolding of RNA pseudoknots | Q28257841 | ||
| The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data | Q28271703 | ||
| Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs | Q29617637 | ||
| Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation | Q30402159 | ||
| RNA 3D structure prediction by using a coarse-grained model and experimental data | Q30593882 | ||
| Forced-unfolding and force-quench refolding of RNA hairpins | Q33233771 | ||
| RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme | Q33364669 | ||
| Predicting loop-helix tertiary structural contacts in RNA pseudoknots | Q33658469 | ||
| Theoretical frameworks for multiscale modeling and simulation | Q33693246 | ||
| How RNA folds | Q33767912 | ||
| RNA pseudoknots: folding and finding | Q33865596 | ||
| Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules | Q33901748 | ||
| On the significance of an RNA tertiary structure prediction | Q33913266 | ||
| A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting | Q33944010 | ||
| Metal ions and RNA folding: a highly charged topic with a dynamic future | Q33986235 | ||
| Fast folding of RNA pseudoknots initiated by laser temperature-jump | Q34035046 | ||
| Predicting ion binding properties for RNA tertiary structures | Q34099007 | ||
| Computational modeling of RNA 3D structures, with the aid of experimental restraints | Q34122757 | ||
| Modeling nucleic acids | Q34271167 | ||
| Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus | Q34362504 | ||
| SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction | Q34505971 | ||
| Clustering to identify RNA conformations constrained by secondary structure | Q34621190 | ||
| Salt contribution to RNA tertiary structure folding stability | Q35079364 | ||
| Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot | Q35647681 | ||
| RNA helix stability in mixed Na+/Mg2+ solution | Q35753774 | ||
| Improved prediction of RNA tertiary structure with insights into native state dynamics | Q35775755 | ||
| Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints | Q35783573 | ||
| Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA. | Q35842560 | ||
| Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation | Q35869391 | ||
| Structure Prediction of RNA Loops with a Probabilistic Approach | Q36096150 | ||
| Automated and fast building of three-dimensional RNA structures | Q36316650 | ||
| RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. | Q36376536 | ||
| Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. | Q50771785 | ||
| A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect. | Q51038351 | ||
| Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. | Q51921832 | ||
| The thermodynamics and kinetics of a nucleotide base pair. | Q52669707 | ||
| Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations. | Q53398707 | ||
| Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. | Q53416576 | ||
| Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. | Q54839487 | ||
| Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot | Q73435111 | ||
| Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: the role of magnesium ions in stability | Q77569533 | ||
| The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain | Q79503470 | ||
| Atomistic analysis of pseudoknotted RNA unfolding | Q83891265 | ||
| Coarse-grained model for predicting RNA folding thermodynamics | Q86487529 | ||
| Kinetic regulation mechanism of pbuE riboswitch | Q86500112 | ||
| Computational study of stability of an H-H-type pseudoknot motif | Q87074808 | ||
| A nucleotide-level coarse-grained model of RNA | Q88127110 | ||
| Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex | Q88732466 | ||
| Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA. | Q36425977 | ||
| Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions | Q36429548 | ||
| Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms | Q36666278 | ||
| Role of ion valence in the submillisecond collapse and folding of a small RNA domain | Q36697486 | ||
| Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency | Q36740765 | ||
| Bridging the gap in RNA structure prediction. | Q36769213 | ||
| Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel. | Q36949444 | ||
| Predicting structures and stabilities for H-type pseudoknots with interhelix loops. | Q37142084 | ||
| Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting | Q37293094 | ||
| Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron | Q37393597 | ||
| Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures | Q37394795 | ||
| Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation | Q37426607 | ||
| Graph-based sampling for approximating global helical topologies of RNA. | Q37660036 | ||
| Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations | Q37744021 | ||
| The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots | Q38290170 | ||
| Ab initio RNA folding | Q38494122 | ||
| Progress and Current Challenges in Modeling Large RNAs | Q38639057 | ||
| RNA Structure: Advances and Assessment of 3D Structure Prediction | Q38855997 | ||
| The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides | Q39750514 | ||
| Challenges in RNA Structural Modeling and Design | Q40120319 | ||
| Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions | Q40188511 | ||
| Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis. | Q40950675 | ||
| Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension | Q41504071 | ||
| Predicting RNA pseudoknot folding thermodynamics | Q42530587 | ||
| New metrics for comparing and assessing discrepancies between RNA 3D structures and models | Q42554029 | ||
| Physics-based de novo prediction of RNA 3D structures. | Q42712420 | ||
| Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae | Q44108217 | ||
| Mechanical unfolding of the beet western yellow virus -1 frameshift signal. | Q44210564 | ||
| Salt contribution to the flexibility of single-stranded nucleic acid offinite length | Q45739309 | ||
| All-atom knowledge-based potential for RNA structure prediction and assessment | Q45783105 | ||
| Nanopore electric snapshots of an RNA tertiary folding pathway. | Q46689139 | ||
| Opportunities and Challenges in RNA Structural Modeling and Design | Q47566705 | ||
| Radial distribution function of semiflexible oligomers with stretching flexibility | Q47817725 | ||
| Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling | Q47910968 | ||
| Martini Coarse-Grained Force Field: Extension to RNA. | Q47998413 | ||
| Structure modeling of RNA using sparse NMR constraints. | Q49519923 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 6 | |
| P304 | page(s) | e1006222 | |
| P577 | publication date | 2018-06-07 | |
| P1433 | published in | PLOS Computational Biology | Q2635829 |
| P1476 | title | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions | |
| P478 | volume | 14 |
| Q57455867 | Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions | cites work | P2860 |
Search more.