منابع مشابه
RNA pseudoknots: folding and finding
RNA pseudoknots are important for function. Three-dimensional structural information is available, insights into factors affecting pseudoknot stability are being reported, and computer programs are available for predicting pseudoknots.
متن کاملPseudoknots in RNA folding landscapes
MOTIVATION The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground...
متن کاملBiphasic folding kinetics of RNA pseudoknots and telomerase RNA activity.
Using a combined master equation and kinetic cluster approach, we investigate RNA pseudoknot folding and unfolding kinetics. The energetic parameters are computed from a recently developed Vfold model for RNA secondary structure and pseudoknot folding thermodynamics. The folding kinetics theory is based on the complete conformational ensemble, including all the native-like and non-native states...
متن کاملFolding and finding RNA secondary structure.
Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that function...
متن کاملConserved RNA Pseudoknots
Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle. Techniques for detecting evolutionarily conserved, and hence most likely functional RNA pseudoknots, are therefore of interest. Here we present an extension of the alidot approach that extracts conserved seconda...
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ژورنال
عنوان ژورنال: F1000 Biology Reports
سال: 2010
ISSN: 1757-594X
DOI: 10.3410/b2-8