RNA 3D structure prediction by using a coarse-grained model and experimental data. Xia, Z., Bell, D., Shi, Y., & Ren, P. The journal of physical chemistry. B, February, 2013. ![RNA 3D structure prediction by using a coarse-grained model and experimental data. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model were able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg2+ cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.
@article{Xia2013,
title = {{RNA} {3D} structure prediction by using a coarse-grained model and experimental data.},
issn = {1520-5207},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23438338},
doi = {10.1021/jp400751w},
abstract = {RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model were able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg2+ cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.},
journal = {The journal of physical chemistry. B},
author = {Xia, Zhen and Bell, David and Shi, Yue and Ren, Pengyu},
month = feb,
year = {2013},
pmid = {23438338},
keywords = {\#nosource},
}
Downloads: 0
{"_id":"Gs9cbb3Jh5gPXi9Ph","bibbaseid":"xia-bell-shi-ren-rna3dstructurepredictionbyusingacoarsegrainedmodelandexperimentaldata-2013","author_short":["Xia, Z.","Bell, D.","Shi, Y.","Ren, P."],"bibdata":{"bibtype":"article","type":"article","title":"RNA 3D structure prediction by using a coarse-grained model and experimental data.","issn":"1520-5207","url":"http://www.ncbi.nlm.nih.gov/pubmed/23438338","doi":"10.1021/jp400751w","abstract":"RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model were able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg2+ cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.","journal":"The journal of physical chemistry. B","author":[{"propositions":[],"lastnames":["Xia"],"firstnames":["Zhen"],"suffixes":[]},{"propositions":[],"lastnames":["Bell"],"firstnames":["David"],"suffixes":[]},{"propositions":[],"lastnames":["Shi"],"firstnames":["Yue"],"suffixes":[]},{"propositions":[],"lastnames":["Ren"],"firstnames":["Pengyu"],"suffixes":[]}],"month":"February","year":"2013","pmid":"23438338","keywords":"#nosource","bibtex":"@article{Xia2013,\n\ttitle = {{RNA} {3D} structure prediction by using a coarse-grained model and experimental data.},\n\tissn = {1520-5207},\n\turl = {http://www.ncbi.nlm.nih.gov/pubmed/23438338},\n\tdoi = {10.1021/jp400751w},\n\tabstract = {RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model were able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg2+ cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.},\n\tjournal = {The journal of physical chemistry. B},\n\tauthor = {Xia, Zhen and Bell, David and Shi, Yue and Ren, Pengyu},\n\tmonth = feb,\n\tyear = {2013},\n\tpmid = {23438338},\n\tkeywords = {\\#nosource},\n}\n\n","author_short":["Xia, Z.","Bell, D.","Shi, Y.","Ren, P."],"key":"Xia2013","id":"Xia2013","bibbaseid":"xia-bell-shi-ren-rna3dstructurepredictionbyusingacoarsegrainedmodelandexperimentaldata-2013","role":"author","urls":{"Paper":"http://www.ncbi.nlm.nih.gov/pubmed/23438338"},"keyword":["#nosource"],"metadata":{"authorlinks":{}},"html":""},"bibtype":"article","biburl":"https://bibbase.org/zotero/eric.larG4","dataSources":["4i5C7S78DvJNsaHyg","5L2zM5wNE5CBYNuea"],"keywords":["#nosource"],"search_terms":["rna","structure","prediction","using","coarse","grained","model","experimental","data","xia","bell","shi","ren"],"title":"RNA 3D structure prediction by using a coarse-grained model and experimental data.","year":2013}