VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability.
RNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. The prediction of the structure and folding stability of RNA-RNA complexes is a problem of significant biological importance and receives substantial interes...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5033388?pdf=render |
| _version_ | 1818547036098658304 |
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| author | Xiaojun Xu Shi-Jie Chen |
| author_facet | Xiaojun Xu Shi-Jie Chen |
| author_sort | Xiaojun Xu |
| collection | DOAJ |
| description | RNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. The prediction of the structure and folding stability of RNA-RNA complexes is a problem of significant biological importance and receives substantial interest in the biological community. The VfoldCPX server provides a new web interface to predict the two-dimensional (2D) structures of RNA-RNA complexes from the nucleotide sequences. The VfoldCPX server has several novel advantages including the ability to treat RNAs with tertiary contacts (crossing base pairs) such as loop-loop kissing interactions and the use of physical loop entropy parameters. Based on a partition function-based algorithm, the server enables prediction for structure with and without tertiary contacts. Furthermore, the server outputs a set of energetically stable structures, ranked by their stabilities. The results allow users to gain extensive physical insights into RNA-RNA interactions and their roles in RNA function. The web server is freely accessible at "http://rna.physics.missouri.edu/vfoldCPX". |
| first_indexed | 2024-12-12T08:01:14Z |
| format | Article |
| id | doaj.art-ab48c6d8632c433bb359f9be2613901d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T08:01:14Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ab48c6d8632c433bb359f9be2613901d2022-12-22T00:32:08ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01119e016345410.1371/journal.pone.0163454VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability.Xiaojun XuShi-Jie ChenRNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. The prediction of the structure and folding stability of RNA-RNA complexes is a problem of significant biological importance and receives substantial interest in the biological community. The VfoldCPX server provides a new web interface to predict the two-dimensional (2D) structures of RNA-RNA complexes from the nucleotide sequences. The VfoldCPX server has several novel advantages including the ability to treat RNAs with tertiary contacts (crossing base pairs) such as loop-loop kissing interactions and the use of physical loop entropy parameters. Based on a partition function-based algorithm, the server enables prediction for structure with and without tertiary contacts. Furthermore, the server outputs a set of energetically stable structures, ranked by their stabilities. The results allow users to gain extensive physical insights into RNA-RNA interactions and their roles in RNA function. The web server is freely accessible at "http://rna.physics.missouri.edu/vfoldCPX".http://europepmc.org/articles/PMC5033388?pdf=render |
| spellingShingle | Xiaojun Xu Shi-Jie Chen VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. PLoS ONE |
| title | VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. |
| title_full | VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. |
| title_fullStr | VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. |
| title_full_unstemmed | VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. |
| title_short | VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. |
| title_sort | vfoldcpx server predicting rna rna complex structure and stability |
| url | http://europepmc.org/articles/PMC5033388?pdf=render |
| work_keys_str_mv | AT xiaojunxu vfoldcpxserverpredictingrnarnacomplexstructureandstability AT shijiechen vfoldcpxserverpredictingrnarnacomplexstructureandstability |