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Protein secondary structure prediction
Current Opinion in Structural Biology, 1995The past year has seen a consolidation of protein secondary structure prediction methods. The advantages of prediction from an aligned family of proteins have been highlighted by several accurate predictions made 'blind', before any X-ray or NMR structure was known for the family.
S R, Krystek, W J, Metzler, J, Novotny
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Nature, 1975
NUMEROUS attempts have been made to deduce a secondary structure of 5S RNA1–4. Differing approaches have yielded various structures, but each turns out to be inconsistent with either physical, chemical, biochemical, or comparative evidence. Clearly the situation is not analogous to that which obtained for transfer RNA (tRNA).
G E, Fox, C R, Woese
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NUMEROUS attempts have been made to deduce a secondary structure of 5S RNA1–4. Differing approaches have yielded various structures, but each turns out to be inconsistent with either physical, chemical, biochemical, or comparative evidence. Clearly the situation is not analogous to that which obtained for transfer RNA (tRNA).
G E, Fox, C R, Woese
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Secondary structure of halorhodopsin
Biochemistry, 1986Ultraviolet circular dichroism (CD) spectroscopy in the interval from 190 to 240 nm has been used to estimate the secondary structural content of halorhodopsin (hR), a light-driven chloride pump isolated from the membranes of Halobacterium halobium. Least-squares curve fitting of the CD spectrum for hR solubilized with octyl glucoside yields an alpha ...
B K, Jap, S H, Kong
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Mathematical Biosciences, 1991
A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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2015
A topological RNA structure is derived from a diagram, and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological information, and for a fixed topological genus there exist only finitely many such shapes.
Qijun He, Matthew Macauley, Robin Davies
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A topological RNA structure is derived from a diagram, and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological information, and for a fixed topological genus there exist only finitely many such shapes.
Qijun He, Matthew Macauley, Robin Davies
+5 more sources
Targeting DNA Secondary Structures
Current Medicinal Chemistry, 2000DNA secondary structures containing regions of single-stranded DNA have now been identified in the genomic DNA of a number of prokaryotic and eukaryotic species, including humans. Many of these secondary structures are associated with regions of DNA involved in regulation of transcription: promoters or upstream elements.
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Protein Secondary Structure Prediction
2009While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary ...
Pirovano, W.A., Heringa, J.
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RNA Secondary Structure Thermodynamics
2012Several different ways to predict RNA secondary structures have been suggested in the literature. Statistical methods, such as those that utilize stochastic context-free grammars (SCFGs), or approaches based on machine learning aim to predict the best representative structure for the underlying ensemble of possible conformations.
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2006
The three-dimensional structures of nucleic acids, RNA, and DNA, are dominated by double-helical regions that are formed by canonical Watson–Crick and wobble (GU) base pairs, which collectively are referred to as the secondary structure of the molecule.
Ivo L. Hofacker +2 more
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The three-dimensional structures of nucleic acids, RNA, and DNA, are dominated by double-helical regions that are formed by canonical Watson–Crick and wobble (GU) base pairs, which collectively are referred to as the secondary structure of the molecule.
Ivo L. Hofacker +2 more
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2010
There are several methods available that can be used to gain information on secondary structure, apart from X-ray crystallography, which remains the ‘gold standard’.
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There are several methods available that can be used to gain information on secondary structure, apart from X-ray crystallography, which remains the ‘gold standard’.
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