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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
TLDR
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization and experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions. Expand
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
TLDR
The details of the free energy rules and of the latest version 3.0 software are described and future plans are also discussed. Expand
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy incrementsExpand
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
TLDR
Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs, and on average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within the limit of the model. Expand
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
TLDR
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces and predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions. Expand
Improved free-energy parameters for predictions of RNA duplex stability.
TLDR
These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C, about as good as can be expected from the nearest-neighbor model. Expand
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
TLDR
Dynalign is a new computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. Expand
Improved predictions of secondary structures for RNA.
TLDR
The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70% and the excellent performance is consistent with these interactions being the primary interactions determiningRNA secondary structure. Expand
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For eachExpand
Predicting thermodynamic properties of RNA.
Publisher Summary This chapter discusses the thermodynamic properties of RNA and explores the rules governing the folding of biological molecules into their three-dimensional structures. RNA is anExpand
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