Journal ArticleDOI
The Computer Simulation of RNA Folding Pathways Using a Genetic Algorithm
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TLDR
It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions, suggesting that RNA folding kinetics is very important for the formation of functional RNA structures.About:
This article is published in Journal of Molecular Biology.The article was published on 1995-06-30. It has received 332 citations till now. The article focuses on the topics: Non-coding RNA & RNA.read more
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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
TL;DR: 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.
Journal ArticleDOI
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
David H. Mathews,Matthew D. Disney,Jessica L. Childs,Susan J. Schroeder,Michael Zuker,Douglas H. Turner +5 more
TL;DR: 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 increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch.
Journal ArticleDOI
A dynamic programming algorithm for RNA structure prediction including pseudoknots
Elena Rivas,Sean R. Eddy +1 more
TL;DR: This is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model and a useful graphical representation borrowed from quantum field theory is adopted.
Journal ArticleDOI
Dengue Virus Structural Differences That Correlate with Pathogenesis
Katrin C. Leitmeyer,David W. Vaughn,Douglas M. Watts,Rosalba Salas,Iris Villalobos,de Chacon,Celso Ramos,Rebeca Rico-Hesse +7 more
TL;DR: A method for comparing dengue type 2 genomes (reverse transcriptase PCR in six fragments) directly from patient plasma is developed to better reflect the true composition of viral RNA populations in the natural host and permit their association with pathogenesis.
Journal ArticleDOI
Hierarchy and dynamics of rna folding
Philippe Brion,Eric Westhof +1 more
TL;DR: Recent data point to the central controlling and monitoring roles of RNA-binding proteins that can bind to the different folding stages, either before full establishment of the secondary structure or at the molten globule state before the cooperative transition to the final three-dimensional structure.
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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
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