Results 11 to 20 of about 1,640,958 (330)
RNA secondary structure design [PDF]
Physical Review E, 2006 We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called designable.
A. K. Hartmann +8 more
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Alternate RNA Structures [PDF]
Cold Spring Harbor Perspectives in Biology, 2020 RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome.
Marie Teng-Pei, Wu, Victoria, D'Souza
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Topology of RNA-RNA Interaction Structures [PDF]
Journal of Computational Biology, 2012 40 pages 15 ...
Andersen, Jørgen E. +3 more
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Counting RNA Pseudoknotted Structures [PDF]
Journal of Computational Biology, 2011 In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the
Saule, Cédric +3 more
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RNA Secondary Structure Prediction [PDF]
Current Protocols in Nucleic Acid Chemistry, 2000 AbstractDetails for predicting secondary structure of RNA sequences using free energy minimization are given. Protocols present the use of the RNAstructure computer program (for PCs) and the mfold server (for Unix platforms). The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted.
Mathews, David H. +2 more
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Irreducibility in RNA Structures [PDF]
Bulletin of Mathematical Biology, 2009 In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various distributions: of the numbers of irreducible substructures, their locations and sizes, parameterized in terms of ...
Jin, Emma Y., Reidys, Christian M.
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Canonical RNA Pseudoknot Structures [PDF]
Journal of Computational Biology, 2008 21 pages,7 ...
Ma, Gang, Reidys, Christian M.
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SS/SW BASE PAIRS ARE THE ONLY BASE PAIRS INVOLVED IN LONG-RANGE RNA TERTIARY MOTIFS
Journal of Bioinformatics and Genomics, 2020 The structure of noncoding RNAs largely determines their functions. With the rapid growth of experimental data on the RNA secondary structures, the task of predicting its spatial structure becomes the most urgent task of RNA bioinformatics.
Manakov, A.K. +2 more
doaj +1 more source
Fundamental Research, 2022 To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts ...
Meiling Piao +12 more
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RNA STRUCTURAL SEGMENTATION [PDF]
, 2009 We describe several dynamic programming segmentation algorithms to segment RNA secondary and tertiary structures into distinct domains. For this purpose, we consider fitness functions that variously depend on (i) base pairing probabilities in the Boltzmann low energy ensemble of structures, (ii) contact maps inferred from 3-dimensional structures, and (
Ivan, Dotú +3 more
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