ArticleMethods in molecular biology (Clifton, N.J.)2015
A Method to Predict the 3D Structure of an RNA Scaffold.
Article in Methods in molecular biology (Clifton, N.J.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase.Nucleic acids research · 2020Article
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.The journal of physical chemistry. B · 2018Article
- RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.RNA (New York, N.Y.) · 2017Article
- Structural computational modeling of RNA aptamers.Methods (San Diego, Calif.) · 2016Article
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Authors and funding
2 authors.
Funding
Abstract
The ever increasing discoveries of noncoding RNA functions draw a strong demand for RNA structure determination from the sequence. In recently years, computational studies for RNA structures, at both the two-dimensional and the three-dimensional levels, led to several highly promising new developments. In this chapter, we describe a recently developed RNA structure prediction method based on the virtual bond-based coarse-grained folding model (Vfold). The main emphasis in the Vfold method is placed on the loop entropy calculations, the treatment of noncanonical (mismatch) interactions and the 3D structure assembly from motif-based template library. As case studies, we use the glycine riboswitch and the G310-U376 domain of MLV RNA to illustrate the Vfold-based prediction of RNA 3D structures from the sequences.
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Registered trials
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