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Transient RNA–protein interactions in RNA folding [PDF]
FEBS Journal, 2011 The RNA folding trajectory features numerous off‐pathway folding traps, which represent conformations that are often equally as stable as the native functional ones. Therefore, the conversion between these off‐pathway structures and the native correctly folded ones is the critical step in RNA folding. This process, referred to as RNA refolding, is slow,
Boris Fürtig, Renée Schroeder
exaly +4 more sources
Perspectives on Viral RNA Genomes and the RNA Folding Problem [PDF]
Viruses, 2020 Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles.
Susan J. Schroeder
doaj +2 more sources
A comparison of RNA folding measures [PDF]
BMC Bioinformatics, 2005 Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences.
Gardner Paul P +2 more
doaj +4 more sources
RNA Chaperones and the RNA Folding Problem [PDF]
Journal of Biological Chemistry, 1995 Functional and structural inter-relationships of RNA and proteins in the execution and control of biological processes such as RNA processing, RNA splicing, and translation are increasingly apparent. In this minireview, I present an RNA chaperone hypothesis, which fosters the view that constraints imposed by fundamental problems in the folding of RNA ...
Daniel Herschlag
openaire +3 more sources
Protein solubility and folding enhancement by interaction with RNA. [PDF]
PLoS ONE, 2008 While basic mechanisms of several major molecular chaperones are well understood, this machinery has been known to be involved in folding of only limited number of proteins inside the cells. Here, we report a chaperone type of protein folding facilitated
Seong Il Choi +12 more
doaj +1 more source
Folding Kinetics of Large RNAs [PDF]
Journal of Molecular Biology, 2008 We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. These blocks correspond to subsequences and their thermodynamically optimal structures. These are determined by the standard dynamic programming approach to RNA folding.
Wolfinger, Michael +8 more
openaire +3 more sources
Complete probabilistic analysis of RNA shapes [PDF]
, 2006 Voß B, Giegerich R, Rehmsmeier M. Complete probabilistic analysis of RNA shapes. BMC Biology. 2006;4(1): 5.Background: Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically ...
Marc Rehmsmeier +8 more
core +1 more source
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs [PDF]
, 2010 Theis C, Janssen S, Giegerich R. Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. In: Moulton V, Singh M, eds. Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Lecture Notes in Bioinformatics. Vol
Corinna Theis +7 more
core +1 more source
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
doaj +1 more source
A comprehensive comparison of comparative RNA structure prediction approaches [PDF]
, 2004 Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004;5(1): 140.Background: An increasing number of researchers have released novel RNA structure analysis and prediction ...
Giegerich, R. +7 more
core +1 more source