Advances and opportunities in RNA structure experimental determination and computational modeling

J Zhang, Y Fei, L Sun, QC Zhang - Nature methods, 2022 - nature.com
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Geometric deep learning of RNA structure

RJL Townshend, S Eismann, AM Watkins, R Rangan… - Science, 2021 - science.org
RNA molecules adopt three-dimensional structures that are critical to their function and of
interest in drug discovery. Few RNA structures are known, however, and predicting them …

trRosettaRNA: automated prediction of RNA 3D structure with transformer network

W Wang, C Feng, R Han, Z Wang, L Ye, Z Du… - Nature …, 2023 - nature.com
RNA 3D structure prediction is a long-standing challenge. Inspired by the recent
breakthrough in protein structure prediction, we developed trRosettaRNA, an automated …

When will RNA get its AlphaFold moment?

B Schneider, BA Sweeney, A Bateman… - Nucleic Acids …, 2023 - academic.oup.com
The protein structure prediction problem has been solved for many types of proteins by
AlphaFold. Recently, there has been considerable excitement to build off the success of …

Genome-wide map** of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

I Manfredonia, C Nithin… - Nucleic acids …, 2020 - academic.oup.com
SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA
genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of …

Accurate RNA 3D structure prediction using a language model-based deep learning approach

T Shen, Z Hu, S Sun, D Liu, F Wong, J Wang, J Chen… - Nature …, 2024 - nature.com
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved
challenge. Determining RNA 3D structures is crucial for understanding their functions and …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
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 …

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 …

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

Y Li, C Zhang, C Feng, R Pearce… - Nature …, 2023 - nature.com
RNAs are fundamental in living cells and perform critical functions determined by their
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …