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12/01/2024, The trRosettaRNA server (as 'Yang-Server') was ranked 4th among 64 participating groups (1st among 16 Server groups) in the CASP16 RNA prediction experiment.; 11/01/2024, …

Wang J, Mao K, Zhao Y, Zeng C, Xiang J, Zhang Y, Xiao Y. Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct …

Nov 9, 2023 · RNA 3D structure prediction is a long-standing challenge. Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, an automated deep …

RNA 3D structure editing. The group of tools aims to facilitate operations on RNA 3D structure. Concatenate merge a bunch of PDB files into one file ... The RNAComposer system offers a …

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction. …

Explore RNAComposer for one-click prediction of RNA 3D structure! ... the fastest in its class and most user-friendly computational tool to be found internet-wide; publicly available and freely …

Nov 25, 2024 · RhoFold+ is a computational tool for RNA 3D structure prediction, built using RNA-specific insights and data. It leverages a large RNA language model (RNA-FM) for sequence …

IsRNA is a coarse-grained model for de novo prediction and blind screening of RNA 3D structures. The model has three main features: a four/five-bead coarse-grained representation …

During the last decade, a good number of RNA 3D structure prediction algorithms have been actively developed and improved. These prediction methods cover approaches similar to …

a, The architecture of RhoFold+, a fully automated and differentiable end-to-end approach to de novo RNA 3D structure prediction from the sequence.Using an RNA language model (RNA …

Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The …

This is an alternative method for structure prediction that may have higher fidelity in structure prediction. Multilign Predict low free energy secondary structures common to three or more …

Since the knowledge of the 3D structures of RNAs is a fundamental prerequisite to completely understand the functions of RNAs. In this work, we have integrated the existing RNA 3D …

Rather, the prediction confidence for the pre-let-7a component within BioRNA (Figure 5C) by AlphaFold 3 was lower than the pre-let-7a itself (Figure 4D), underscoring the complexities …

Sep 24, 2024 · In this review, Mukherjee et al. discuss the latest computational methods for RNA 3D structure prediction in light of outcomes from the RNA-Puzzles and CASP prediction …

2 days ago · Their technique can predict thousands of structures in just minutes, making it much speedier than existing experimental methods for analyzing the structures. Using this …

Jan 28, 2023 · In an RNA 3D structure prediction evaluation, we have a list of predicted structures and at least one reference structure available. ... rna-tools is a set of RNA structure tools, …

The rna-tools package was used in various scientific projects, to calculate stability of various U6 RNAs of the spliceosome , to process input files for SimRNAweb (RNA 3D structure prediction …

Jan 8, 2025 · It has 20 nonredundant single-stranded RNAs. For each RNA, 40 decoys are generated with four RNA 3D structure prediction models The decoys are not as near to native …

1 day ago · Second, in contrast to other tools 5,6,7,8,9,10, RiboTIE constructs ORFs after the prediction step rather than before it. Specifically, RiboTIE processes ribosome information …

Dec 4, 2019 · INTRODUCTION. RNA 3D structure prediction, which dates back to the late 1960s (), is nowadays being widely studied with the help of computer science.An increasing number …

Jan 10, 2025 · Deep learning methods have emerged as powerful tools for modeling protein-RNA interactions. Early models like DeepBind utilized convolutional neural networks to predict the …

2 days ago · Chemists have found a new way to determine 3D genome structures, using generative AI, that can predict thousands of genome structures in minutes, making it much …