Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides
MC Hopfinger, CC Kirkpatrick… - Nucleic Acids …, 2020 - academic.oup.com
The most popular RNA secondary structure prediction programs utilize free energy (Δ G° 37)
minimization and rely upon thermodynamic parameters from the nearest neighbor (NN) …
minimization and rely upon thermodynamic parameters from the nearest neighbor (NN) …
Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction
J Zuber, BJ Cabral, I McFadyen, DM Mauger… - Rna, 2018 - rnajournal.cshlp.org
RNA secondary structure prediction is often used to develop hypotheses about structure-
function relationships for newly discovered RNA sequences, to identify unknown functional …
function relationships for newly discovered RNA sequences, to identify unknown functional …
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures
Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary
structure prediction and to model thermodynamic ensembles of secondary structures. The …
structure prediction and to model thermodynamic ensembles of secondary structures. The …
[HTML][HTML] A test and refinement of folding free energy nearest neighbor parameters for RNA including N6-methyladenosine
M Szabat, M Prochota, R Kierzek, E Kierzek… - Journal of Molecular …, 2022 - Elsevier
RNA folding free energy change parameters are widely used to predict RNA secondary
structure and to design RNA sequences. These parameters include terms for the folding free …
structure and to design RNA sequences. These parameters include terms for the folding free …
Blind tests of RNA nearest-neighbor energy prediction
The predictive modeling and design of biologically active RNA molecules requires
understanding the energetic balance among their basic components. Rapid developments …
understanding the energetic balance among their basic components. Rapid developments …
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model
A Spasic, KD Berger, JL Chen, MG Seetin… - Nucleic Acids …, 2018 - academic.oup.com
RNA folding free energy change nearest neighbor parameters are widely used to predict
folding stabilities of secondary structures. They were determined by linear regression to …
folding stabilities of secondary structures. They were determined by linear regression to …
Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters
JL Chen, AL Dishler, SD Kennedy, I Yildirim, B Liu… - Biochemistry, 2012 - ACS Publications
Thermodynamic parameters for GU pairs are important for predicting the secondary
structures of RNA and for finding genomic sequences that code for structured RNA. Optical …
structures of RNA and for finding genomic sequences that code for structured RNA. Optical …
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
DH Mathews - Rna, 2004 - rnajournal.cshlp.org
A partition function calculation for RNA secondary structure is presented that uses a current
set of nearest neighbor parameters for conformational free energy at 37° C, including …
set of nearest neighbor parameters for conformational free energy at 37° C, including …
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects
Nearest neighbor parameters for estimating the folding stability of RNA secondary structures
are in widespread use. For helices, current parameters penalize terminal AU base pairs …
are in widespread use. For helices, current parameters penalize terminal AU base pairs …
[HTML][HTML] Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
An improved dynamic programming algorithm is reported for RNA secondary structure
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …