Rna folding
A simple, practical and complete O -time Algorithm for RNA folding using the Four-Russians Speedup
... an RNA sequence of length n, is at the heart of almost all methods to computationally predict RNA secondary structure, including more complex methods that incorporate more realistic folding models, ...
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Faster algorithms for RNA-folding using the Four-Russians method
... As mentioned earlier, the cells of a diagonal are inde- pendent of one another and can be computed in parallel. In Stojanovski et al. [7], elements of the diagonal are assigned to a block of threads. This design does not ...
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Sparse RNA folding revisited: space-efficient minimum free energy structure prediction
... MFE folding of RNAs while guaranteeing pre- diction of the MFE ...of RNA folding such as base pair maximization, but emerges only in realistic free energy minimization ...pseudoknot-free RNA ...
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RNA folding with hard and soft constraints
... The framework of ADP [12] makes it transparent that the structure of recursion is determined by the grammar that is used to generate the search space. This structure is also exposed explicitly when stochastic ...
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An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding
... than from sequence alone. While there have been advances in methods that provide structure experimen- tally, the need for computational prediction has grown as the gap between sequence availability and structure has ...
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Spiraling Complexity: A Test of the Snowball Effect in a Computational Model of RNA Folding
... found in our simulations. However, an evolution experi- ment in S. cerevisiae detected a simple DMI between two lineages that had only accumulated six unique mutations each ðk ¼ 12Þ (Anderson et al. 2010). This indicates ...
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Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments
... of RNA-RNA contacts in the presence of ...affect RNA binding by NSP2 octamers (Figure 1—figure supplement 4A), nor had it any effect on the apparent S11:S5 CCF amplitude (Figure 1—figure supplement ...
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Human Immunodeficiency Virus Type 1 Vif Protein Is an Integral Component of an mRNP Complex of Viral RNA and Could Be Involved in the Viral RNA Folding and Packaging Process
... strong RNA binding ...the RNA binding ...weak RNA binding activity ...decreased RNA binding activity (Table 2). It is notable that no identified RNA binding domains are similar to the ...
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Effect of Population Size and Mutation Rate on the Evolution of RNA Sequences on an Adaptive Landscape Determined by RNA Folding
... We used only non-modified ribonucleotides [76–79], i.e. A, C, G and U, in our discrete-time simulations of RNA sequence evolution. Any one evolving population initially consisted of identical sequences whose MFE ...
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Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments
... segmented RNA viruses, including RVs, Bluetongue virus (BTV) and influenza A viruses (IAVs), may control selection of the correct RNA segments (Fajardo et ...S10 RNA have been shown to be involved in ...
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RNA folding in Drosophila shows a distance effect for compensatory fitness interactions.
... The phylogenetic analysis was done manually based on the following criterion: a putative helix was considered “proven” if two or more covariations, caused by independ- en[r] ...
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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
... for RNA-RNA interaction predic- tions is usually handled with a class of approaches that simultaneously predict a common structure for both RNAs including their ...usual RNA folding methods ...
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Defining the RNA-Protein Interactions in the Trypanosome Preribosomal Complex
... L5. RNA folding predictions (with Mfold [26]) based on thermodynamics showed that loop A/stem V and the ␥ arm can fold the same as in the full-length 5S rRNA, but an oligonucleotide spanning the sequence of ...
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Research on folding diversity in statistical learning methods for RNA secondary structure prediction
... of RNA folding rules is confirmed by dimension reduction and cluster analysis, and the relationship between folding rules and family is also ...the RNA function in the same ...the ...
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Chang, Hung-Chun (2007): Mechanisms of de novo multi-domain protein folding in bacteria and eukaryotes. Dissertation, LMU München: Fakultät für Chemie und Pharmazie
... rapid folding mechanism, we first compared the kinetics of translation and folding in the bacterial S30 lysate with those in a rabbit reticulocyte ...in folding yield in both systems (~5% in S30 ...
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Inverse folding of RNA pseudoknot structures
... Background: RNA exhibits a variety of structural ...of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is ...
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Origami Theory David Dureisseix pdf
... by folding an edge, or a crease, back on itself and we can bisect a right angle (or any other angle) by placing the folds that form the two sides of the angle on top of each ...of folding angles of 60 or 30 ...
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Topological complexity, contact order, and protein folding rates
... protein folding kinetics and the native state equilibrium properties ...protein folding, both in theory and ...the folding of pro- tein molecules larger than about 100 amino acids, whose kinetics is ...
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Modulation of a protein free-energy landscape by circular permutation
... A circular permutation is a rearrangement of the connectivity of a protein obtained by linking the N- and C-termini of a protein with a peptide linker and creating new termini elsewhere. Circular permutations can occur ...
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To a new hardware design methodology: A case study of the cochlea model
... The implementation of the cochlea model proved more difficult than expected. Because it is a computationally intensive model with a wide range of input values, a large word-length and a lot of multipliers are needed. ...
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