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 …
RNA 3D structure prediction using coarse-grained models
The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to
understanding their various and important biological functions. However, experimental …
understanding their various and important biological functions. However, experimental …
IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures
Modeling structures and functions of large ribonucleic acid (RNAs) especially with
complicated topologies is highly challenging due to the inefficiency of large conformational …
complicated topologies is highly challenging due to the inefficiency of large conformational …
In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers
Nucleic acid aptamers hold great promise for therapeutic applications due to their favorable
intrinsic properties, as well as high-throughput experimental selection techniques. Despite …
intrinsic properties, as well as high-throughput experimental selection techniques. Despite …
Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA
G Bagnolini, TTB Luu, AE Hargrove - RNA, 2023 - rnajournal.cshlp.org
RNA structures regulate a wide range of processes in biology and disease, yet small
molecule chemical probes or drugs that can modulate these functions are rare. Machine …
molecule chemical probes or drugs that can modulate these functions are rare. Machine …
Predicting the effect of single mutations on protein stability and binding with respect to types of mutations
The development of methods and algorithms to predict the effect of mutations on protein
stability, protein–protein interaction, and protein–DNA/RNA binding is necessitated by the …
stability, protein–protein interaction, and protein–DNA/RNA binding is necessitated by the …
Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
RNA molecules cannot fold in the absence of counterions. Experiments are typically
performed in the presence of monovalent and divalent cations. How to treat the impact of a …
performed in the presence of monovalent and divalent cations. How to treat the impact of a …
IsRNA: An iterative simulated reference state approach to modeling correlated interactions in RNA folding
Coarse-grained RNA folding models promise great potential for RNA structure prediction. A
key component in a coarse-grained folding model is the force field. One of the challenges in …
key component in a coarse-grained folding model is the force field. One of the challenges in …
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 …
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 …