Xiao Yi

Dr. Xiao received his master's degree in Theoretical Biophysics from Institute of Biophysics of Chinese Academy of Science, Beijing, China, in 1984 and his doctoral degree in Theoretical Physics from Shanghai Jiao Tong University, Shanghai, China, in 1988. He is presently a Professor in the School of Physics, Huazhong University of Science and Technology, Wuhan, China. He has conducted a series of research programs including NSFC and his research interests include protein and RNA folding mechanism and prediction of three-dimensional structures, interactions and functions of nucleic acids.

Academic Degrees

Ph.D. degree in Theoretical Physics, 1988, Shanghai Jiao Tong University.

Professional Experience

1993-Present: Professor, Huazhong University of Science and Technology;

1991-1993: Associate Professor, Huazhong University of Science and Technology;

Selected Publications

1. Ercheng Wang, Jun Wang, Changjun Chen, Y. Xiao*. Computational evidence that fast translation speed can increase the probability of cotranslational protein folding. Scientific Reports. 5:15316 (2015).

2. Jun Wang, Yunjie Zhao, Jian Wang, Yi Xiao*. Computational study of stability of an H-H-type pseudoknot motif. Physical Review E92: 062705 (2015).

3. Jian Wang, Yunjie Zhao, Chunyan Zhu and Yi Xiao*. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Researche. 43:e63 (2015).

4. Gong, Z., Y. Zhao, C. Chen, Y. Duan, Y. Xiao*. Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations. PLoS One. 9(3), e92247, 2014.

5. Chen C., Y. Huang, X. Jiang and Y. Xiao*, A fast tomographic method for searching the minimum free energy path, J. Chem. Phys. 141, 154109 (2014);

6. Zhou, R., Maisuradze, G. G., Sunol, D., Todorovski, T., Macias, M. J., Xiao, Y., Scheraga, H. A., Czaplewski, C. & Liwo, A. (2014). Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proc Natl Acad Sci U S A 111, 18243-8.

7. Huang, Y., S. Liu, D. Guo, L. Li andY. Xiao*(2013). A novel protocol for three-dimensional structure prediction of RNA-protein complexes.Sci Rep3: 1887.



8. Guo, D., S. Liu, Y. Huang andY. Xiao*(2013). Preorientation of protein and RNA just before contacting.J Biomol Struct Dyn31(7): 716-728.



9. Chen, C., E. Wang, P. Liu andY. Xiao*(2013). Simulation study of the role of the ribosomal exit tunnel on protein folding.Phys Rev E87(2): 022701.



10. Chen, C., Y. Huang andY. Xiao*(2013). Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.J Biomol Struct Dyn31(2): 206-214.



11. Chen, C., Y. Huang, X. Jiang andY. Xiao*(2013). Binding free-energy calculation of an ion-peptide complex by constrained dynamics.Phys Rev E87(6): 062705.



12. Chen, C., Y. Huang, X. Ji andY. Xiao*(2013). Efficiently finding the minimum free energy path from steepest descent path. J Chem Phys138(16): 164122.



13. Li, L., Y. Huang,Y. Xiao*(2013). How to use not-always-reliable binding site information in protein-protein docking prediction.Plos One8, e75936.



14. Zhao Y., J. Wang, X. Chen, H. Luo, Y. Zhao,Y. Xiao*and R. Chen* (2013). Large-scale study of long non-coding RNA functions based on structure and expression features.Sci China Life Sci56(10): 953-959.

15. Zhao, Y., Y. Huang, Z. Gong, Y. Wang, J. Man andY. Xiao*(2012). Automated and fast building of three-dimensional RNA structures.Sci Rep2: 734.

16. Wu, D., H. Li, W. Du, X. Ji, W. Liu, S. Huang andY. Xiao*(2012). Mathematical modeling of therapeutic strategies for myeloid malignancies.Pathol Oncol Res18(4): 939-947.

17. Maisuradze, G. G., R. Zhou, A. Liwo,Y. Xiaoand H. A. Scheraga (2012). Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain.J Mol Biol420(4-5): 350-365.

18. Jiang, X., A. Zhong, C. Chen, Y. Huang andY. Xiao*(2012). Network approach to identify the folding transition states of peptides and proteins.Phys Rev E86(5 Pt 1): 051901.

19. Gong, Z., Y. Zhao, C. Chen andY. Xiao*(2012). Computational study of unfolding and regulation mechanism of preQ1 riboswitches.Plos One7(9): e45239.

20. Chen, C., Y. Huang andY. Xiao*(2012). Free-energy calculations along a high-dimensional fragmented path with constrained dynamics.Phys Rev E86(3 Pt 1): 031901.

21. Zhou R, He Y,Xiao Y*(2011)Multi-nucleation and vectorial folding pathways of large helix protein.Comput Biol Chem35: 169-173.

22. Gong Z, Zhao Y, Chen C,Xiao Y*(2011) Role of Ligand Binding in Structural Organization of Add A-riboswitch Aptamer: A Molecular Dynamics Simulation.J Biomol Struct Dyn29: 403-416.

23. Li L, Guo D, Huang Y, Liu S,Xiao Y*(2011) ASPDock: protein-protein docking algorithm using atomic solvation parameters model.BMC Bioinformatics12:36.

24. Zhao Y, Gong Z,Xiao Y*(2011) Improvements of the hierarchical approach for predicting RNA tertiary structure.J Biomol Struct Dyn28: 815-826.

25. Lei HX, Chen CJ,Xiao Yand Duan Y (2011) The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel.J Chem Phys134: 205104-1-7.

26. Fleishman SJ et al (2011) Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.J Mol Bio414:289-302.

27. Feng J, M Li, YZ Huang andY Xiao*(2010) Symmetric key structural residues in symmetric proteins with beta-trefoil fold."PLoS One5: e14138.

28. Wang G, C. Du, Chen, H., Simha, R., Rong,Y., Xiaoand C. Zeng (2010) Process-based network decomposition reveals backbone motif structure.Proc Natl Acad Sci U S A107(23): 10478-83.

29. Gong Z, Zhao Y,Xiao Y*(2010) RNA stability under different combinations of amber force fields and solvation models.J Biomol Struct Dyn28: 431-441.

30. Chen CJ andY Xiao*. (2010). Accurate free energy calculation along optimized paths.J Comput Chem. 31:1368-1375.

31. Jiang XW, Changjun Chen,Y Xiao*. (2010) Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins.J Comput Chem. 31: 2502-2509.

Selected Cases

Awards and Honors

• National Natural Science Foundation of China , Grant No.11374113;

• National Natural Science Foundation of China , Grant No.31570722;

Courses Taught

• Theoretical Mechanics;

• Biophysics.