ArticleBiophysics reports
Physics-based RNA structure prediction.
Article in Biophysics reports. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- The life and death of RNA across temperatures.Computational and structural biotechnology journal · 2022Review
- Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.Nucleic acids research · 2020Article
- 3dRNA: Building RNA 3D structure with improved template library.Computational and structural biotechnology journal · 2020Article
- RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.Nature communications · 2019Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.Journal of molecular biology · 2017Article
- Opportunities and Challenges in RNA Structural Modeling and Design.Biophysical journal · 2017Article
- Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis.Nucleic acids research · 2017Article
- Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.RNA (New York, N.Y.) · 2017Article
- Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA.PloS one · 2017Article
- PAI: Predicting adenosine to inosine editing sites by using pseudo nucleotide compositions.Scientific reports · 2016Article
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Authors and funding
2 authors.
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Abstract
Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures' predictions and then focus on a recently developed RNA statistical mechanical model-the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.