3dDNA: A Computational Method of Building DNA 3D Structures
Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the numbe...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/18/5936 |
| _version_ | 1827658392142872576 |
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| author | Yi Zhang Yiduo Xiong Yi Xiao |
| author_facet | Yi Zhang Yiduo Xiong Yi Xiao |
| author_sort | Yi Zhang |
| collection | DOAJ |
| description | Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains. |
| first_indexed | 2024-03-09T23:01:09Z |
| format | Article |
| id | doaj.art-7ec6010595fb48599eaa03f2e69699cb |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T23:01:09Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-7ec6010595fb48599eaa03f2e69699cb2023-11-23T18:01:38ZengMDPI AGMolecules1420-30492022-09-012718593610.3390/molecules271859363dDNA: A Computational Method of Building DNA 3D StructuresYi Zhang0Yiduo Xiong1Yi Xiao2School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, ChinaSchool of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, ChinaSchool of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, ChinaConsiderable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains.https://www.mdpi.com/1420-3049/27/18/59363dDNADNA3D template libraries3D structure prediction |
| spellingShingle | Yi Zhang Yiduo Xiong Yi Xiao 3dDNA: A Computational Method of Building DNA 3D Structures Molecules 3dDNA DNA 3D template libraries 3D structure prediction |
| title | 3dDNA: A Computational Method of Building DNA 3D Structures |
| title_full | 3dDNA: A Computational Method of Building DNA 3D Structures |
| title_fullStr | 3dDNA: A Computational Method of Building DNA 3D Structures |
| title_full_unstemmed | 3dDNA: A Computational Method of Building DNA 3D Structures |
| title_short | 3dDNA: A Computational Method of Building DNA 3D Structures |
| title_sort | 3ddna a computational method of building dna 3d structures |
| topic | 3dDNA DNA 3D template libraries 3D structure prediction |
| url | https://www.mdpi.com/1420-3049/27/18/5936 |
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