3dRNA/DNA is an automatic, fast, and high-accuracy RNA and DNA tertiary structure prediction method. It uses sequence and secondary structure information to build three dimensional structures of RNA and DNA from template segments.
The main routines for 3dRNA/DNA is:
- Break the given secondary structure into smallest secondary elements (SSEs).
- Find the template of these SSEs from our templates library, which is built from crystal or NMR structures. If the template is missing, a distance-geometry-based loop building method can be used to build the SSE ab initio.
- The assembling module is the structure assembled by templates searched for each SSE. The assembling module do not consider pseudoknots.
- The optimizing module is the structure optimized from the assembling module or a given structure by using Simulated Annealing Monte Carlo method. This process can further optimize the module with constraints of pseudoknots, residue-residue interactions or distances by using a coarse-grained energy function.
Cite Our Work
- Zhao Y, Huang Y, Gong Z, Wang Y, Man J, Xiao Y. Automated and fast building of three-dimensional RNA structures. Sci Rep. 2012;2:734.
- Wang J, Zhao Y, Zhu C, Xiao Y. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Res. 2015 May 26;43(10):e63.
- Wang J, Mao K, Zhao Y, Zeng C, Xiang J, Zhang Y, Xiao Y. Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis. Nucleic Acids Res. 2017 Jun 20;45(11):6299-6309.
- Wang J, Wang J, Huang Y, Xiao Y. 3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction. Int J Mol Sci. 2019 Aug 23;20(17):4116.
- Zhang Y, Wang J, Xiao Y. 3dRNA: Building RNA 3D structure with improved template library. Comput Struct Biotechnol J. 2020 Aug 28;18:2416-2423.
- Zhang Y, Wang J, Xiao Y. 3dRNA: 3D Structure Prediction from Linear to Circular RNAs. J Mol Biol. 2022 Jun 15;434(11):167452.
- Zhang Y, Xiong Y, Xiao Y. 3dDNA: A Computational Method of Building DNA 3D Structures. Molecules. 2022 Sep 13;27(18):5936.