Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

K Leppek, R Das, M Barna - Nature reviews Molecular cell biology, 2018‏ - nature.com
RNA molecules can fold into intricate shapes that can provide an additional layer of control
of gene expression beyond that of their sequence. In this Review, we discuss the current …

High-throughput determination of RNA structures

EJ Strobel, AM Yu, JB Lucks - Nature Reviews Genetics, 2018‏ - nature.com
RNA performs and regulates a diverse range of cellular processes, with new functional roles
being uncovered at a rapid pace. Interest is growing in how these functions are linked to …

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

K Leppek, GW Byeon, W Kladwang… - Nature …, 2022‏ - nature.com
Therapeutic mRNAs and vaccines are being developed for a broad range of human
diseases, including COVID-19. However, their optimization is hindered by mRNA instability …

FARFAR2: improved de novo rosetta prediction of complex global RNA folds

AM Watkins, R Rangan, R Das - Structure, 2020‏ - cell.com
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang… - Nature …, 2020‏ - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-
dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy …

Inferring protein 3D structure from deep mutation scans

NJ Rollins, KP Brock, FJ Poelwijk, MA Stiffler… - Nature …, 2019‏ - nature.com
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka… - Rna, 2017‏ - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …

3D RNA and functional interactions from evolutionary couplings

C Weinreb, AJ Riesselman, JB Ingraham, T Gross… - Cell, 2016‏ - cell.com
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far
outpaces the research on the structure and functional interactions of these RNA gene …

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

M Magnus, MJ Boniecki, W Dawson… - Nucleic acids …, 2016‏ - academic.oup.com
RNA function in many biological processes depends on the formation of three-dimensional
(3D) structures. However, RNA structure is difficult to determine experimentally, which has …

Computer-aided design of RNA-targeted small molecules: A growing need in drug discovery

J Manigrasso, M Marcia, M De Vivo - Chem, 2021‏ - cell.com
In recent years, researchers have identified certain RNAs as druggable targets for small
molecules to treat several human pathologies. However, these regulatory RNAs are …