| Chapter title |
A Method to Predict the 3D Structure of an RNA Scaffold
|
|---|---|
| Chapter number | 1 |
| Book title |
RNA Scaffolds
|
| Published in |
Methods in molecular biology, January 2015
|
| DOI | 10.1007/978-1-4939-2730-2_1 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-2729-6, 978-1-4939-2730-2
|
| Authors |
Xiaojun Xu, Shi-Jie Chen, Xu, Xiaojun, Chen, Shi-Jie |
| 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. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 11 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 3 | 27% |
| Student > Ph. D. Student | 2 | 18% |
| Professor | 1 | 9% |
| Unspecified | 1 | 9% |
| Student > Bachelor | 1 | 9% |
| Other | 1 | 9% |
| Unknown | 2 | 18% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 4 | 36% |
| Agricultural and Biological Sciences | 3 | 27% |
| Unspecified | 1 | 9% |
| Physics and Astronomy | 1 | 9% |
| Unknown | 2 | 18% |