RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Computational modeling of RNA 3D structure based on experimental data
A Ponce-Salvatierra, Astha, K Merdas… - Bioscience …, 2019 - portlandpress.com
RNA molecules are master regulators of cells. They are involved in a variety of molecular
processes: they transmit genetic information, sense cellular signals and communicate …
processes: they transmit genetic information, sense cellular signals and communicate …
RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling
RNA 3D structures are critical for understanding their functions. However, only a limited
number of RNA structures have been experimentally solved, so computational prediction …
number of RNA structures have been experimentally solved, so computational prediction …
[HTML][HTML] 3dRNA: Building RNA 3D structure with improved template library
Y Zhang, J Wang, Y **ao - Computational and structural biotechnology …, 2020 - Elsevier
Most of computational methods of building RNA tertiary structure are template-based. The
template-based methods usually can give more accurate 3D structures due to the use of …
template-based methods usually can give more accurate 3D structures due to the use of …
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation
YL Tan, X Wang, YZ Shi, W Zhang, ZJ Tan - Biophysical Journal, 2022 - cell.com
Abstract Knowledge-based statistical potentials have been shown to be rather effective in
protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical …
protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical …
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation
of RNA designed for structure prediction and refinement. In our approach, the representation …
of RNA designed for structure prediction and refinement. In our approach, the representation …
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-
dimensional (3D) structures and stability play essential roles in a variety of biological …
dimensional (3D) structures and stability play essential roles in a variety of biological …
Ab initio predictions for 3D structure and stability of single-and double-stranded DNAs in ion solutions
ZC Mu, YL Tan, BG Zhang, J Liu… - PLOS Computational …, 2022 - journals.plos.org
The three-dimensional (3D) structure and stability of DNA are essential to
understand/control their biological functions and aid the development of novel materials. In …
understand/control their biological functions and aid the development of novel materials. In …
Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway
L **, YL Tan, Y Wu, X Wang, YZ Shi, ZJ Tan - RNA, 2019 - rnajournal.cshlp.org
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene
expression, and their structures and stability are critical to their biological functions. In this …
expression, and their structures and stability are critical to their biological functions. In this …
Salt-dependent RNA pseudoknot stability: effect of spatial confinement
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly
affect the folded structures and stability of RNAs. The emergence of RNA-driven phase …
affect the folded structures and stability of RNAs. The emergence of RNA-driven phase …