Secondary structures
Physicochemical Position-Dependent Properties in the Protein Secondary Structures
... the secondary structures, including helical segments, β-strands, and tight turns (δ-turns, γ- turns, β-turns, α-turns, and π-turns) in contrast to the few limited structures that were considered in ...
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Random generation of RNA secondary structures according to native distributions
... RNA secondary structures are used for predicting the structure of a given RNA sequence (see ...that secondary structure prediction methods based on random sampling represent a non-deterministic ...
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Mechanism of ribosome translation through mRNA secondary structures
... dependence of the translation rate on the force applied to the ends of the mRNA duplex to unzip the duplex was elaborately determined by Qu et al. [3]. With smFRET by monitoring efficiencies of FRET between the two tRNAs ...
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CMD: a database to store the bonding states of cysteine motifs with secondary structures
... their secondary structures and propensity value assignments, and the ability to query using Protein IDs and motif sequences is a novel and significant feature over prior prediction works which use ...
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Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures
... RNA structures has made them tRNAs and rRNAs that have highly conserved structures a suitable model for the study of compensatory evolu- (Woese and Pace 1993; Dirheimer et ...1990; secondary ...
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A specific orientation of RNA secondary structures is required for initiation of reverse transcription.
... As well as the interaction of the PBS with the tRNA primer, there are a series of secondary structures, U5-IR stem, U5-leader stem, and U5 RNA-T4iC interaction region, all required for e[r] ...
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Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures
... To account for the conformational statistics associated with an ensemble of secondary structures, it is useful (28,40–43) to represent the RNA secondary structure as a tree graph (44), i.e., a ...
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The Bovine Leukemia Virus Encapsidation Signal Is Composed of RNA Secondary Structures
... stem-loop structures in the primary encapsidation signal re- duced the replication efficiency by a factor of 7 or 40, respec- ...stem-loop structures relative to RW 1, ...stem-loop structures ...
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Mechanisms of obtaining secondary structures on
... Keywords: aluminum alloys; bronze; journal bearings; tribological alloys; friction; friction surface; 20.. secondary structures; self-organization.[r] ...
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Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
... A major obstacle is that, at present, there is no gen- eral and efficient way to link smFRET measurements to interpretations in terms of explicit molecular structures. To solve this problem, a natural first step ...
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Secondary structures in polyoma DNA.
... Several lines of evidence indicate that the inverted repeat stems of the two secondary-structure loops lie in the regions of polyoma virus DNA flanking and probably very close to the seq[r] ...
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Ebola Virus VP30 Is an RNA Binding Protein
... RNA secondary structure (27, ...these secondary structures is not known, the transcriptional activity of EBOV requires VP30 and the presence of sequences surrounding the transcription initiation site ...
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5.8S rRNA Sequence and Secondary Structure in Parabronema skrjabini and Related Habronematidae Species
... the secondary structure was ...ondary structures (default settings, with T = 37 ...sumptive secondary structures were then calculated with mfold at the DNA ...
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Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets
... gene was found clustered with other tRNA genes, but the locations of trnM 1 were variable over species. Another case of tRNA gene duplication is the trnD in M. yessoensis, which is found in single copy in the mitogenomes ...
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Predicting Βeta Turns and Βeta Turn Types Using a Novel Over Sampling Approach
... predicted secondary structures of protein were effective in predicting β -turns and their types [7] [9] [12] [14] [23], the way of classifying a secondary structure of protein into three states of ...
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Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation.
... helical secondary structures in three-dimensional structures of polypeptide chains is a different ...helical secondary structures are outlined in the following ...
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Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
... were detected as frequently as expected by chance, contradicting our initial prediction that they would be subject to detectable purifying selection. Indeed, an analysis of mutation saturation revealed that three out of ...
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Secondary Structural Elements within the 3′ Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA
... for secondary-structure mapping by limited RNase digestion be- cause this region contains two host protein binding elements identified by our ...stable secondary structures, and of the three models ...
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Bioinformatics analysis of metallothionein gene from Agaricus bisporus, Ganoderma lucidum, Taiwanofungus camphorates and Paxillus involutus
... The secondary structures of AbMT, GlMT, TcMT and PiMT amino acid sequences were predicted using SOPM online ...The secondary structure analysis showed 4 MT proteins were relatively rich in random ...
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The Relationship Between Third-Codon Position Nucleotide Content, Codon Bias, mRNA Secondary Structure and Gene Expression in the Drosophilid Alcohol Dehydrogenase Genes Adh and Adhr
... mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree ...
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