Secondary structure
The circular secondary structure uncertainty plot (CS2-UPlot) - visualizing RNA secondary structure with base pair binding probabilities
... mfe secondary structure is known and typically repre- sented as a ...mfe secondary structure representation of the RNA sequence on a circular plot much in the same fashion as Circos [ 1 ] ...
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Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution
... protein structure for over four ...to secondary structure and are largely free from the influence of side-chain ...measure structure in ...of secondary structures in the infrared ...
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Analysis of an optimal hidden Markov model for secondary structure prediction
... for secondary structure prediction [30] convinced us that highly connected mod- els are more appropriate in our ...for secondary structure prediction might be a problem when employing such a ...
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Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.
... ary structure has been noticed early ...objective secondary struc- ture assignment was not a trivial task, due to the variations observed in secondary structures when compared to ideal ...the ...
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An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.
... Following secondary structure models for the 18S rRNA molecule, available in the Euro- pean Ribosomal Database [59], two partitions or charac- ter groups were assigned to the sequences: (1) paired stem – ...
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Predicting secondary structure propensities in IDPs using simple statistics from three-residue fragments
... main secondary structural elements: α-helices and extended ...the secondary structural element, even though the method operates from structural preferences of three-residue ...state-of-the-art ...
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CHARACTERIZING ALTERATIONS IN THE SECONDARY STRUCTURE OF TYPICAL PROTEINS UNDER EXPOSURE TO ELECTROMAGNETIC FIELDS
... the secondary structure of proteins, such as it was demonstrated in previous literature (Elliot and Ambrose, 1950; Ambrose and Elliot, 1951; Elliot, ...
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Secondary-structure characterization by far-UV CD of highly purified uncoupling protein 1 expressed in yeast
... Secondary structure of UCP1–His 6 by far-UV CD CD spectroscopy was accordingly used to determine the second- ary structure of the DDM-purified UCP1–His 6 as well as the possible conformational ...
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Comparison of the Sequences of Class a β-lactamase and of the Secondary Structure Elements of Penicillin-Recognizing Proteins
... We propose that, in addition to the ABL consensus numbering scheme (2), the numbering of class A secondary structure elements also be adopted for all active serine penicillin-recognizing[r] ...
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Towards a Weighted-Tree Similarity Algorithm for RNA Secondary Structure Comparison
... acid) secondary structure comparison is ...RNA secondary structure are represented as normalized node-weighted ...RNA secondary structures are informative and ...RNA secondary ...
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VARNA: Interactive drawing and editing of the RNA secondary structure.
... circular representation draws the backbone on a circle while connecting partners with chords; the planar graph representation uses predefined distances between neighboring paired bases, while limiting the structural ...
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Unfolding RNA 3D structures for secondary structure prediction benchmarking
... details about how these algorithms are designed, there are excellent primers [44] and detailed accounts [8] written by dynamic programming adepts. The limitations of current single-sequence approaches are somewhat ...
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Extending the Hardness of RNA Secondary Structure Comparison
... RNA secondary structure comparison is essential for (i) identification of highly conserved structures during evolution (which cannot always be detected in the primary sequence, since it is often ...
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Multi-dimensional probing for RNA secondary structure(s) prediction
... RNA secondary structure Keywords : RNA structure, sampling, probing data, SHAPE, mutational profil, clustering Abstract : In structural bioinformatics, predicting the secondary ...
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NMR secondary structure and interactions of recombinant human MOZART1 protein, a component of the gamma-tubulin complex
... initial structure characterization The optimized NMR conditions where the MOZART1 protein was solubilized in sulfobetaine-12 micelles allowed us to record the 3D NMR experiments neces- sary for protein resonance ...
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Design evaluation of naval combatant secondary structure under hydrostatic lateral load
... Boundary conditions for the bulkhead and deckhead were varied with the bare plate analysis to reveal that the maximum effective stress concentration was consistently expe[r] ...
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Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing
... Figure 7. Structural and primary-sequence features important for human pri-miRNA processing. (A) Summary of human pri-miRNA determinants identified or confirmed in this study. (B) Processing enhancement from adding ...
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Modeling protein evolution using secondary structures
... 4.5. Secondary structure ...i) secondary structure table, which includes all the secondary structure information extracted from PDB as well as distance to the surface; and ii) ...
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Designing RNA Secondary Structures Is Hard
... into secondary structures where some bases match one another while others remain ...Pseudoknot-free secondary structures can be represented as well-parenthesized expressions with additional dots, where ...
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Spitzer Secondary Eclipses of WASP-18b
... Subject headings: planets and satellites: atmospheres — planets and satellites: composition — planets and satellites: individual (WASP-18b) — infrared: planetary systems 1. INTRODUCTION Among the more than 500 extrasolar ...
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