Theory and modeling of RNA structure and interactions with metal ions and small molecules

LZ Sun, D Zhang, SJ Chen - Annual review of biophysics, 2017 - annualreviews.org
In addition to continuous rapid progress in RNA structure determination, probing, and
biophysical studies, the past decade has seen remarkable advances in the development of …

Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies

EC Morishita - Expert Opinion on Drug Discovery, 2023 - Taylor & Francis
Introduction The field of RNA-targeted small molecules is rapidly evolving, owing to the
advances in experimental and computational technologies. With the identification of several …

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

T Puton, LP Kozlowski, KM Rother… - Nucleic acids …, 2013 - academic.oup.com
We present a continuous benchmarking approach for the assessment of RNA secondary
structure prediction methods implemented in the CompaRNA web server. As of 3 October …

IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures

D Zhang, J Li, SJ Chen - Journal of chemical theory and …, 2021 - ACS Publications
Modeling structures and functions of large ribonucleic acid (RNAs) especially with
complicated topologies is highly challenging due to the inefficiency of large conformational …

Coarse-grained HiRE-RNA model for ab initio RNA folding beyond simple molecules, including noncanonical and multiple base pairings

T Cragnolini, Y Laurin, P Derreumaux… - Journal of chemical …, 2015 - ACS Publications
HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study
of RNA folding. Using a reduced set of particles and detailed interactions accounting for …

Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter

W Lu, Y Tang, H Wu, H Huang, Q Fu, J Qiu, H Li - BMC bioinformatics, 2019 - Springer
Background RNA secondary structure prediction is an important issue in structural
bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP …

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches1

KJ Purzycka, M Popenda, M Szachniuk, M Antczak… - Methods in …, 2015 - Elsevier
Understanding the numerous functions of RNAs depends critically on the knowledge of their
three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of …

Mutation in the 3'untranslated region of APP as a genetic determinant of cerebral amyloid angiopathy

G Nicolas, D Wallon, C Goupil, AC Richard… - European Journal of …, 2016 - nature.com
Aβ-related cerebral amyloid angiopathy (CAA) is a major cause of primary non-traumatic
brain hemorrhage. In families with an early onset of the disease, CAA can be due to amyloid …

Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume

P Li, T Zheng, L Li, X Zhuo, L Jiang, J Wang, T Cheng… - PeerJ, 2019 - peerj.com
Prunus mume is an important ornamental woody plant that grows in tropical and subtropical
regions. Freezing stress can adversely impact plant productivity and limit the expansion of …

FMRP regulates actin filament organization via the armadillo protein p0071

A Nolze, J Schneider, R Keil, M Lederer, S Hüttelmaier… - Rna, 2013 - rnajournal.cshlp.org
Loss of fragile X mental retardation protein (FMRP) causes synaptic dysfunction and
intellectual disability. FMRP is an RNA-binding protein that controls the translation or …