Results 31 to 40 of about 1,301,283 (332)
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 (
William Andrew Lorenz +3 more
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It's a loop world – single strands in RNA as structural and functional elements
Biomolecular Concepts, 2011 Unpaired regions in RNA molecules – loops – are centrally involved in defining the characteristic three-dimensional (3D) architecture of RNAs and are of high interest in RNA engineering and design.
Schudoma Christian
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VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. [PDF]
PLoS ONE, 2016 RNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. The prediction of the structure and folding stability of RNA-RNA complexes is a problem of significant ...
Xiaojun Xu, Shi-Jie Chen
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On Topological RNA Interaction Structures [PDF]
Journal of Computational Biology, 2013 Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ ...
Qin, Jing, Reidys, Christian
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RNApolis: Computational Platform for RNA Structure Analysis
Foundations of Computing and Decision Sciences, 2019 In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created.
Szachniuk Marta
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Structure of an Archaeal RNA Polymerase [PDF]
Journal of Molecular Biology, 2008 Related multisubunit RNA polymerases (RNAPs) carry out gene transcription in all kingdoms of life. Since structural information is limited to bacterial and eukaryotic RNAPs, we determined the cryo-electron microscopic structure of the RNAP from the thermophilic archaeon Pyrococcus furiosus at 13 A resolution.
Kusser, A. +6 more
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Nature Communications, 2018 The mitochondrial RNA degradosome (mtEXO) plays an essential role in the regulation of mitochondrial gene expression and is composed of the 3′-to-5′ exoribonuclease Dss1 and the helicase Suv3.
Michal Razew +12 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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, 1991 This chapter describes the RNA structural characteristics that have emerged so far. Folded RNA molecules are stabilized by a variety of interactions, the most prevalent of which are stacking and hydrogen bonding between bases. Many interactions among backbone atoms also occur in the structure of tRNA, although they are often ignored when considering ...
Ignacio Tinoco, Michael Chastain
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EMBO Molecular Medicine, 2017 Matrix metalloproteinase 9 (MMP‐9) has recently emerged as a molecule that contributes to pathological synaptic plasticity in schizophrenia, but explanation of the underlying mechanisms has been missing.
Katarzyna Lepeta +10 more
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