Yi Zhang, Jun Wang, Yi Xiao(2022). "3dRNA: 3D structure prediction from linear to circular RNAs." Journal of Molecular Biology. doi:10.1016/j.jmb.2022.167452
Yi Zhang#, Jun Wang#, Yi Xiao(2020). "3dRNA: Building RNA 3D structure with improved template library." Computational and Structural Biotechnology Journal. 18:2416-2423.
Wang J, Wang J, Huang Y, et al(2019). "3dRNA v2. 0: An Updated Web Serverfor RNA 3D Structure Prediction." International journal of molecularsciences 20(17): 4116.
Huang, Y., H. Li and Y. Xiao (2018). "3dRPC: a web server for 3D RNA-protein structure prediction." Bioinformatics 34(7): 1238-1240.
Wang, J. and Y. Xiao (2017). "Using 3dRNA for RNA 3-D Structure Prediction and Evaluation." Curr Protoc Bioinformatics 57: 5 9 1-5 9 12.
Wang, J., K. Mao, Y. Zhao, C. Zeng, J. Xiang, Y. Zhang and Y. Xiao (2017). "Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis." Nucleic Acids Res 45(11): 6299-6309.
Wang, J., Y. Zhao, C. Zhu and Y. Xiao (2015). "3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures." Nucleic Acids Res 43(10): e63.
Wang, J., Y. Zhao, J. Wang and Y. Xiao (2015). "Computational study of stability of an H-H-type pseudoknot motif." Phys Rev E Stat Nonlin Soft Matter Phys 92(6): 062705.
Wang, E., J. Wang, C. Chen and Y. Xiao (2015). "Computational evidence that fast translation speed can increase the probability of cotranslational protein folding." Sci Rep 5: 15316.
Huang, Y., S. Liu, D. Guo, L. Li and Y. Xiao (2013). "A novel protocol for three-dimensional structure prediction of RNA-protein complexes." Sci Rep 3: 1887.
Chen, C., E. Wang, P. Liu and Y. Xiao (2013). "Simulation study of the role of the ribosomal exit tunnel on protein folding." Phys Rev E Stat Nonlin Soft Matter Phys 87(2): 022701.
Zhao, Y., Y. Huang, Z. Gong, Y. Wang, J. Man and Y. Xiao (2012). "Automated and fast building of three-dimensional RNA structures." Sci Rep 2: 734.
Gong, Z., Y. Zhao, C. Chen and Y. Xiao (2012). "Computational study of unfolding and regulation mechanism of preQ1 riboswitches." PLoS One 7(9): e45239.
Wang, G., C. Du, H. Chen, R. Simha, Y. Rong, Y. Xiao and C. Zeng (2010). "Process-based network decomposition reveals backbone motif structure." Proc Natl Acad Sci U S A 107(23): 10478-10483.
Xiao, Y., C. Chen and Y. He (2009). "Folding mechanism of beta-hairpin trpzip2: Heterogeneity, transition state and folding pathways." Int J Mol Sci 10(6): 2838-2848.
He, Y., Y. Xiao, A. Liwo and H. A. Scheraga (2009). "Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field." J Comput Chem 30(13): 2127-2135.
Li, M., Y. Huang and Y. Xiao (2008). "Effects of external interactions on protein sequence-structure relations of beta-trefoil fold." Proteins 72(4): 1161-1170.
Chen, C. and Y. Xiao (2008). "Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories." Bioinformatics 24(5): 659-665.
Huang, Y. and Y. Xiao (2007). "Detection of gene duplication signals of Ig folds from their amino acid sequences." Proteins 68(1): 267-272.
Zhang, S. and Y. Xiao (2006). "Quasiperiodic property in Alu repeats." Phys Rev E Stat Nonlin Soft Matter Phys 74(2 Pt 1): 022901.
Chen, C., Y. Xiao and L. Zhang (2005). "A directed essential dynamics simulation of peptide folding." Biophys J 88(5): 3276-3285.