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Predicting RNA pseudoknot folding thermodynamics
TLDR
A folding thermodynamics model is developed that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics and predicts strong sequence-dependent helix-loop competitions in the Pseudoknot stability and the resultant conformational switches between different hairpin and pseudok not structures.
Physics-based de novo prediction of RNA 3D structures.
TLDR
A free energy-based method to predict larger more complex RNA tertiary folds and a key advantage is the statistical mechanical calculation for the conformational entropy of RNA structures, including those with cross-linked loops.
Predicting RNA folding thermodynamics with a reduced chain representation model.
TLDR
Based on the virtual bond representation for the nucleotide backbone, a reduced conformational model for RNA is developed that predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.
Predicting structures and stabilities for H-type pseudoknots with interhelix loops.
TLDR
A predictive model for pseudoknots with interhelix loops that gives conformational entropy, stability, and the free-energy landscape from RNA sequences and may be a solid starting point for first-principles modeling of more complex, larger RNAs.
Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.
TLDR
This work substantially truncates A9, an RNA aptamer to prostate-specific membrane antigen (PSMA), which retains binding activity, functionality, and is amenable to large-scale chemical synthesis for future clinical applications and highlights the utility of existing RNA structural prediction and protein docking techniques that may be generally applicable to developing RNA aptamers optimized for therapeutic use.
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.
TLDR
A first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles, to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations.
A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable.
The 3'-untranslated region (UTR) of the group 2 coronavirus mouse hepatitis virus (MHV) genome contains a predicted bulged stem-loop (designated P0ab), a conserved cis-acting pseudoknot (PK), and a
Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity.
TLDR
The predicted folding and unfolding pathways not only support the proposed role of conformational switch between hairpin and pseudoknot in hTR activity, but also reveal molecular mechanism for the conformationalswitch.
Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.
TLDR
The model predicts that the two distinct experimental structures, the four-helix junction structure and the helix Ib-containing structure, can actually coexist and specifically compete with each other and suggest possible mechanisms for the conformational switches in splicing.
Predicting ribosomal frameshifting efficiency.
TLDR
The free energy landscape analysis leads to a quantitative relationship between the frameshifting efficiency and the tension force generated during the movement of codon-anticodon complexes, which may occur in the A/T to A/A accommodation process or the translocation process, but shows no consistent correlation between frameshifted efficiency and global stability of the downstream mRNA structure.
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