Results 21 to 30 of about 247,454 (281)
RNA folding energy landscapes [PDF]
Proceedings of the National Academy of Sciences, 2000 Using a statistical mechanical treatment, we study RNA folding energy landscapes. We first validate the theory by showing that, for the RNA molecules we tested having only secondary structures, this treatment ( i ) predicts about the same native structures as the Zuker method, and ( ii ...
S J, Chen, K A, Dill
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Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot. [PDF]
PLoS ONE, 2015 How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias ...
Yunqiang Bian +4 more
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On the combinatorics of sparsification [PDF]
, 2012 Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity.
Christian M Reidys +2 more
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Current Protocols in Nucleic Acid Chemistry, 2002 Peer Reviewed ; https://deepblue.lib.umich.edu/bitstream/2027.42/143692/1/cpnc1100 ...
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Current Protocols in Nucleic Acid Chemistry, 2000 AbstractA general overview of the questions and problems in RNA folding is presented. Topics include the differences in the folding problems/questions that apply to RNA versus proteins, methods for determination of final structures, folding versus unfolding, resolution of space and time, and conformational switching.
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SHAPE directed RNA folding [PDF]
Bioinformatics, 2015 Abstract Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable
Luntzer, Dominik +4 more
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TBI server: a web server for predicting ion effects in RNA folding. [PDF]
PLoS ONE, 2015 Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺,
Yuhong Zhu, Zhaojian He, Shi-Jie Chen
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RNA hairpin-folding kinetics [PDF]
Proceedings of the National Academy of Sciences, 2002 Based on the complete ensemble of hairpin conformations, a statistical mechanical model that combines the eigenvalue solutions of the rate matrix and the free-energy landscapes has been able to predict the temperature-dependent folding rate, kinetic intermediates, and folding pathways for hairpin-forming RNA sequences.
Wenbing, Zhang, Shi-Jie, Chen
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Theoretical Search for RNA Folding Nuclei
Entropy, 2015 The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins.
Leonid B. Pereyaslavets +1 more
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Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity.
PLoS ONE, 2010 Due to the energetic frustration of RNA folding, tertiary structured RNA is typically characterized by a rugged folding free energy landscape where deep kinetic barriers separate numerous misfolded states from one or more native states.
Miguel J B Pereira +2 more
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