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- RNA structure prediction is a computational task that aims to predict the 3D arrangement of the helices and the tertiary interactions of RNA molecules1. The prediction methods can be divided into homologous modeling and physics-based modeling1. The methods usually consist of three steps: generating 3D structure ensembles, selecting near-native structures using a scoring function, and refining the structures2. The prediction of RNA secondary structure, which is a prerequisite for 3D structure prediction, is often based on thermodynamic models and dynamic programming3.
Learn more:âś•This summary was generated using AI based on multiple online sources. To view the original source information, use the "Learn more" links.RNA 3D structure prediction mainly involves the 3D arrangement of the helices and the stabilization of the structure with complicated tertiary interactions. Over recent decades, a variety of computational methods have been developed to predict RNA 3D structures, which can be roughly classified into homologous modeling and physics-based modeling.academic.oup.com/nar/article/51/7/3341/7067938In recent decades, various computational models have been developed to predict RNA 3D structures [ 11, 12, 13, 14, 15 ], and the models are generally composed of three procedures: predicting 3D structure ensembles, identifying near-native structures that are close to the experimentally determined native structures through a reliable scoring function/statistical potential, and refining identified near-native structures [ 11, 15...
www.mdpi.com/1420-3049/28/14/5532The conventional computational prediction for RNA secondary structure is based on thermodynamic models to find the minimum free energy through a dynamic programming (DP) approach [ 11, 12 ]. For example, Vienna RNAfold [ 13] and RNAstructure [ 14] are popular methods that use thermodynamic models to predict the secondary structure.bmcbioinformatics.biomedcentral.com/articles/10.1… Accurate RNA 3D structure prediction using a …
Nov 21, 2024 · Here we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences.
RNAfold web server - univie.ac.at
RNAfold web server can calculate the minimum free energy (MFE) and partition function of single stranded RNA or DNA sequences, and generate interactive or colorized plots of the predicted …
List of RNA structure prediction software - Wikipedia
32 rows · This list of RNA structure prediction software is a compilation of software tools and …
See all 32 rows on en.wikipedia.orgNAME DESCRIPTION KNOTS [NOTE 1] LINKS SQUARNA Secondary structure prediction b… Yes sourcecode CentroidFold Secondary structure prediction b… No sourcecode webserver CentroidHomfold Secondary structure prediction b… No sourcecode webserver Context Fold An RNA secondary structure pre… No sourcecode webserver
Welcome to the Mathews Lab RNAstructure Web Servers
RNAstructure Webserver offers various tools for predicting and analyzing RNA secondary structures, such as folding algorithms, partition functions, structure comparisons, and siRNA …
Welcome to the Predict a Secondary Structure Web Server
Feb 14, 2018 · A web server that combines four algorithms to predict and analyze RNA or DNA secondary structures. Users can input a sequence, select options, and receive probability …
trRosettaRNA: automated prediction of RNA 3D structure with …
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 …
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RNA structure prediction by trRosettaRNA - Shandong University
trRosettaRNA is a server that uses a transformer network to predict RNA 3D structures from 2D geometries and secondary structure. It can generate confident models for 263 Rfam families …
Large language modeling and deep learning shed light on RNA …
Nov 21, 2024 · RhoFold+ is a method that we believe will advance the field of RNA 3D structure prediction, showing the best results on CASP15 natural RNA targets (Fig. 1a) and achieving a …
RNAstructure, Version 6.5 - University of Rochester
Jun 12, 2024 · RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including …
DeepFoldRNA: Deep-learning Based RNA Folding and Structure …
DeepFoldRNA is a deep-learning based method for de novo RNA tertiary structure prediction. Starting from an RNA sequence, it first collects an alignment of homologous sequences from …
Geometric deep learning of RNA structure | Science
Aug 26, 2021 · The resulting scoring function, the Atomic Rotationally Equivariant Scorer (ARES), substantially outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction …
RNAComposer
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 …
Predicting RNA structures and functions by artificial intelligence
Jan 1, 2024 · Recent progress in AI-based techniques for predicting RNA structure and function as well as RNA design provide directions and insights for future research on the …
A Method to Predict the 3D Structure of an RNA Scaffold - PMC
3.1 RNA 2D Structure Prediction from the Sequence. The key of the free energy-based RNA 2D structure prediction is the enthalpy and entropy parameters used to evaluate the stability of …
NuFold: end-to-end approach for RNA tertiary structure prediction …
3 days ago · Since NuFold is designed for single chain RNA structure prediction, we adopted the linker trick 48,49,50, where two sequences are connected by dummy sequence and provided …
Accurate RNA 3D structure prediction using a language model …
By integrating an RNA language model pretrained on ~23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end …
UFold: fast and accurate RNA secondary structure prediction with …
Nov 18, 2021 · UFold is a novel method that uses deep learning to predict RNA secondary structure from nucleotide sequences. It outperforms previous methods on within-family …
RNA 3D Structure Prediction: Progress and Perspective - PMC
In this review, we will make a comprehensive overview of the recent advances in RNA 3D structure modeling, including structure ensemble prediction, evaluation, and refinement. …
Advances in the field of RNA 3D structure prediction and …
Sep 24, 2024 · Recent advancements in RNA three-dimensional (3D) structure prediction have provided significant insights into RNA biology, highlighting the essential role of RNA in cellular …
Machine learning in RNA structure prediction: Advances and …
Sep 3, 2024 · The remarkable advancements in machine learning techniques for protein structure prediction have shown promise in the field of RNA structure prediction. In this perspective, we …
Review of machine learning methods for RNA secondary …
Aug 26, 2021 · ML models (trained by wet lab, RNA sequence, or RNA structure data) are directly used to predict RNA secondary structures in an end-to-end way or followed by a filter or …
A deep learning model for characterizing protein-RNA …
Jan 10, 2025 · By framing the problem as a binding affinity prediction from sequence data alone, Reformer delivers precise, base-level insights into RNA-protein interactions. Trained on RNA …
RNA secondary structure prediction using deep learning with ...
Feb 11, 2021 · Inspired by MXfold and the DNN-based RNA secondary structure prediction methods, in this paper, we propose an algorithm for predicting RNA secondary structures …
Mizzou team earns distinction in protein modeling and prediction
1 day ago · The biennial Critical Assessment of Structure Prediction (CASP) aims to advance the field of protein structure prediction. When a protein’s structure is unknown, researchers try to …
The genomes of the most diverse AA genome rice species …
2 days ago · These distinctions underscore the complex interplay of genomic structure and functional dynamics within and across the Oryza species. Gene Prediction and RNA-seq …
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