Reference health
RNAstructure: software for RNA secondary structure prediction and analysis
88/88 checkable references clean · checked 2026-08-03
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
6 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 88 checked references that resolve
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Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs
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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
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Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
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RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
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Improved RNA secondary structure prediction by maximizing expected pair accuracy
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Prediction of RNA secondary structure using generalized centroid estimators
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Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
resolves10.1261/rna.7650904
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
resolves10.1006/jmbi.2001.5351
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences
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Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
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Thermodynamic Prediction of Conserved Secondary Structure: Application to the RRE Element of HIV, the tRNA-like Element of CMV and the mRNA of Prion Protein
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Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of <i>Bombyx mori</i> R2 RNA
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NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon
resolves10.1093/nar/gkn266
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design
resolves10.1186/1471-2105-8-34
Computational RNA secondary structure design: empirical complexity and improved methods
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Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
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Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure
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Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data
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Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
resolves10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G
Complete suboptimal folding of RNA and the stability of secondary structures
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From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
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OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics
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A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
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NMR solution structure of a DNA dodecamer containing single G*T mismatches
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Nearest-Neighbor Thermodynamics of Internal A·C Mismatches in DNA: Sequence Dependence and pH Effects
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Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA
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Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A·A, C·C, G·G, and T·T Mismatches
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Influence of the Oxidatively Damaged Adduct 8-Oxodeoxyguanosine on the Conformation, Energetics, and Thermodynamic Stability of a DNA Duplex
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Deoxydodecanucleotide heteroduplex d(TTTTATAATAAA). d(TTTATTATAAAA) containing the promoter Pribnow sequence TATAAT. I. Double-helix stability by UV spectrophotometry and calorimetry
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The effect of single base‐pair mismatches on the duplex stability of d(T‐A‐T‐T‐A‐A‐T‐A‐T‐C‐A‐A‐G‐T‐T‐G) · d(C‐A‐A‐C‐T‐T‐G‐A‐T‐A‐T‐T‐A‐A‐T‐A)
resolves10.1021/bi00163a019
Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex
resolves10.1021/bi00387a049
Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2
resolves10.1021/bi00183a037
Sequence Specific Thermodynamic and Structural Properties for DNA.cntdot.RNA Duplexes
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Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC
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Application of the Thermodynamic Parameters of DNA Stability Prediction to Double-Helix Formation of Deoxyribooligonucleotides
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Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
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Thermodynamic and structural properties of pentamer DNA.cntdot.DNA, RNA.cntdot.RNA and DNA.cntdot.RNA duplexes of identical sequence
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Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes
resolves10.1021/bi00410a053
Influence of dangling thymidine residues on the stability and structure of two DNA duplexes
resolves10.1093/nar/13.13.4811
Base-base mismatches. Thermodynamics of double helix formation for dCA<sub>3</sub>XA<sub>3</sub>G + dCT<sub>3</sub>YT<sub>3</sub>G (X, Y = A,C,G,D
resolves10.1021/bi9615203
DNA and RNA Oligomer Sequences from the 3‘ Noncoding Region of the Chicken Glutamine Synthetase Gene Form Intramolecular Hairpins
resolves10.1093/nar/21.11.2683
Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding
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Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability
resolves10.1093/nar/20.4.819
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
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Thermodynamic Coupling of the Loop and Stem in Unusually Stable DNA Hairpins Closed by CG Base Pairs
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Selection for Thermodynamically Stable DNA Tetraloops Using Temperature Gradient Gel Electrophoresis Reveals Four Motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc)
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Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges
resolves10.1021/bi00293a016
Unpaired cytosine in the deoxyoligonucleotide duplex dCA3CA3G.cntdot.dCT6G is outside of the helix
resolves10.1021/bi00031a030
Oligonucleotides Containing G.cntdot.A Pairs: Effect of Flanking Sequences on Structure and Stability
resolves10.1093/nar/23.12.2212
Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): unpaired nucleotides can be stabilizing or destabilizing
resolves10.1093/nar/19.4.759
Stability and structure of three-way DNA junctions containing unpaired nucleotides
resolves10.1021/bi00188a011
The Thermodynamics of Formation of a Three-Strand, DNA Three-Way Junction Complex
The 6 references without a DOI — listed, not checked
no DOI — not checkedStorz G, Gottesman S: Versatile Roles of Small RNA Regulators in Bacteria. In The RNA World. third edition. Edited by: Gesteland RF, Cech TR, Atkins JF. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2006:567–594.
no DOI — not checkedPace NR, Thomas BC, Woese CR: Probing RNA structure, function, and history by comparative analysis. In The RNA World. 2nd edition. Edited by: Gesteland RF, Cech TR, Atkins JF. Cold Spring Harbor Laboratory Press; 1999:113–141.
no DOI — not checkedMathews DH, Andre TC, Kim J, Turner DH, Zuker M: An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. In Molecular Modeling of Nucleic Acids. Edited by: Leontis NB, SantaLucia J Jr. American Chemical Society; 1998:246–257.
no DOI — not checkedMathews DH: RNA secondary structure analysis using RNAstructure. In Current Protocols in Bioinformatics. Edited by: Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD, Stormo GD. New York: John Wiley and Sons, Inc; 2006:12.16.11–12.16.14.
no DOI — not checkedMathews DH: Predicting the secondary structure common to two sequences with Dynalign. In Current Protocols in Bioinformatics. Edited by: Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD, Stormo GD. New York: John Wiley and Sons, Inc; 2005:12.14.11–12.14.11.
no DOI — not checkedMathews DH, Turner DH, Zuker M: RNA secondary structure prediction. In Current Protocols in Nucleic Acid Chemistry. Volume 11. Edited by: Beaucage SL, Bergstrum DE, Glick GD, Jones RA. New York: John Wiley and Sons; 2000:2.1–2.10.
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