Structure Prediction of RNA Loops with a Probabilistic Approach.
The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction l...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-08-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC4975501?pdf=render |
| _version_ | 1818007209023373312 |
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| author | Jun Li Jian Zhang Jun Wang Wenfei Li Wei Wang |
| author_facet | Jun Li Jian Zhang Jun Wang Wenfei Li Wei Wang |
| author_sort | Jun Li |
| collection | DOAJ |
| description | The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction. |
| first_indexed | 2024-04-14T05:12:38Z |
| format | Article |
| id | doaj.art-81814a25fe584d1c81a2fa169e4d7192 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-14T05:12:38Z |
| publishDate | 2016-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-81814a25fe584d1c81a2fa169e4d71922022-12-22T02:10:30ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-08-01128e100503210.1371/journal.pcbi.1005032Structure Prediction of RNA Loops with a Probabilistic Approach.Jun LiJian ZhangJun WangWenfei LiWei WangThe knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction.http://europepmc.org/articles/PMC4975501?pdf=render |
| spellingShingle | Jun Li Jian Zhang Jun Wang Wenfei Li Wei Wang Structure Prediction of RNA Loops with a Probabilistic Approach. PLoS Computational Biology |
| title | Structure Prediction of RNA Loops with a Probabilistic Approach. |
| title_full | Structure Prediction of RNA Loops with a Probabilistic Approach. |
| title_fullStr | Structure Prediction of RNA Loops with a Probabilistic Approach. |
| title_full_unstemmed | Structure Prediction of RNA Loops with a Probabilistic Approach. |
| title_short | Structure Prediction of RNA Loops with a Probabilistic Approach. |
| title_sort | structure prediction of rna loops with a probabilistic approach |
| url | http://europepmc.org/articles/PMC4975501?pdf=render |
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