ArticleBiophysical journal2017
Opportunities and Challenges in RNA Structural Modeling and Design.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Amplification-Free Dual-Blocking Autocatalytic CRISPR-Cascade for Atto-Molar DNA Detection with Low Nonspecific Signal.bioRxiv : the preprint server for biology · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.Biophysical journal · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces.Journal of chemical information and modeling · 2024Article
- CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.Nature methods · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.Interdisciplinary sciences, computational life sciences · 2022Article
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
- Small and intermediate size structural RNAs in the unicellular parasiteMicrobial genomics · 2022Article
- Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes.Molecular biology and evolution · 2022Article
- Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- Computational modelling of flavivirus dynamics: The ins and outs.Methods (San Diego, Calif.) · 2021Review
- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- RNA Back to the Spotlight.Journal of structural biology · 2020Article
Corrections and comments
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2 authors.
Funding
Abstract
We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.
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