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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 …

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.

Nov 9, 2023 · Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, an automated deep learning-based approach to RNA 3D structure prediction. …

trRosettaRNA is a deep learning-based algorithm designed for the automated prediction of RNA 3D structures. Utilizing a transformer network, it predicts both 2D inter-nucleotide geometries …

The RNAComposer system offers a new user-friendly approach to the fully automated prediction of large RNA 3D structures. The method is based on the machine translation principle and …

Do you need to get a quick view of RNA 3D fold corresponding to your RNA sequence or secondary structure? Explore RNAComposer for one-click prediction of RNA 3D structure!

Nov 25, 2024 · Predicting RNA 3D structures is critical for understanding its biological functions, advancing RNA-targeted drug discovery, and designing synthetic biology applications. …

NuFold is a state-of-the-art method designed for predicting 3D RNA structures, leveraging deep learning for high accuracy and reliability. This tool is particularly useful for biologists and …

Calculate the sensitivity and positive predictive value (PPV) for a predicted as compared to the accepted structure. Generate a representative sample of structures using stochastic sampling. …

Currently we are hosting 4 web applications for analyzing RNA 3D structure: WebFR3D - server for finding and superimposing RNA 3D motifs; R3D Align - global pairwise alignment of 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 …

Oct 11, 2017 · NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy …

StructRNAfinder - predicts and annotates RNA families in transcript or genome sequences. This single tool not only displays the sequence/structural consensus alignments for each RNA …

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 …

Sep 24, 2024 · We review the outcomes of RNA-Puzzles and critical assessment of structure prediction (CASP) challenges, which assess the state of the field and limitations of existing …

Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and …

Jan 28, 2023 · In this chapter, we illustrate a standard RNA 3D structure prediction assessment protocol using the selected tools from RNA-Puzzles toolkit: rna-tools and RNA_assessment.

RNA secondary structure prediction from a sequence alignment. It uses compensatory base change information as well as energetic considerations to compute a structure. This algorithm …

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 …

Nov 28, 2024 · The RNA language model, complemented with strategies to deal with data scarcity, makes RhoFold+ a fully automated pipeline for RNA 3D structure prediction. It beats …

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 …

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 …