Advances and opportunities in RNA structure experimental determination and computational modeling
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …
include catalyzing biochemical reactions and regulating gene expression. Most of these …
Coarse-grained protein models and their applications
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 …
remains difficult for many protein systems. It is mostly due to the size of protein …
Geometric deep learning of RNA structure
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 …
interest in drug discovery. Few RNA structures are known, however, and predicting them …
trRosettaRNA: automated prediction of RNA 3D structure with transformer network
RNA 3D structure prediction is a long-standing challenge. Inspired by the recent
breakthrough in protein structure prediction, we developed trRosettaRNA, an automated …
breakthrough in protein structure prediction, we developed trRosettaRNA, an automated …
When will RNA get its AlphaFold moment?
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 …
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 …
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
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved
challenge. Determining RNA 3D structures is crucial for understanding their functions and …
challenge. Determining RNA 3D structures is crucial for understanding their functions and …
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 …
FARFAR2: improved de novo rosetta prediction of complex global RNA folds
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …
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
RNAs are fundamental in living cells and perform critical functions determined by their
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …