Chen, C., Xiao, Y., & Huang, Y. (2015). Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space. Phys Rev E Stat Nonlin Soft Matter Phys, 91(5), 052708. doi: 10.1103/PhysRevE.91.052708

Wang, J., Zhao, Y., Zhu, C., & Xiao, Y. (2015). 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Res, 43(10), e63. doi: 10.1093/nar/gkv141

Wang, J., Zhao, Y., Wang, J., & Xiao, Y. (2015). Computational study of stability of an H-H-type pseudoknot motif. Phys Rev E Stat Nonlin Soft Matter Phys, 92(6), 062705. doi: 10.1103/PhysRevE.92.062705

Wang, E., Wang, J., Chen, C., & Xiao, Y. (2015). Computational evidence that fast translation speed can increase the probability of cotranslational protein folding. Sci Rep, 5, 15316. doi: 10.1038/srep15316


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.

Gong, Z., Zhao, Y. J., Chen, C. J., Duan, Y. & Xiao, Y. (2014). Insights into Ligand Binding to PreQ(1) Riboswitch Aptamer from Molecular Dynamics Simulations. Plos One 9.

Chen, C. J., Huang, Y. Z., Jiang, X. W. & Xiao, Y. (2014). A fast tomographic method for searching the minimum free energy path. Journal Of Chemical Physics 141.


Zhao, Y., Wang, J., Chen, X. W., Luo, H. T., Zhao, Y. J., Xiao, Y. & Chen, R. S. (2013). Large-scale study of long non-coding RNA functions based on structure and expression features. Science China-Life Sciences 56, 953-959.

Li, L., Huang, Y. Z. & Xiao, Y. (2013). How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction. Plos One 8.

Huang, Y. Y., Liu, S. Y., Guo, D. C., Li, L. & Xiao, Y. (2013). A novel protocol for three-dimensional structure prediction of RNA-protein complexes. Scientific Reports 3.

Guo, D. C., Liu, S. Y., Huang, Y. Y. & Xiao, Y. (2013). Preorientation of protein and RNA just before contacting. Journal Of Biomolecular Structure & Dynamics 31, 716-728.

Chen, C. J., Wang, E. C., Liu, P. Y. & Xiao, Y. (2013). Simulation study of the role of the ribosomal exit tunnel on protein folding. Physical Review E 87.

Chen, C. J., Huang, Y. Z. & Xiao, Y. (2013). Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath. Journal Of Biomolecular Structure & Dynamics 31, 206-214.

Chen, C. J., Huang, Y. Z., Jiang, X. W. & Xiao, Y. (2013). Binding free-energy calculation of an ion-peptide complex by constrained dynamics. Physical Review E 87.

Chen, C. J., Huang, Y. Z., Ji, X. F. & Xiao, Y. (2013). Efficiently finding the minimum free energy path from steepest descent path. Journal Of Chemical Physics 138.


Zhao, Y., Huang, Y., Gong, Z., Wang, Y., Man, J. & Xiao, Y. (2012). Automated and fast building of three-dimensional RNA structures. Sci Rep 2, 734.

Maisuradze, G. G., Zhou, R., Liwo, A., Xiao, Y. & Scheraga, H. A. (2012). Effects of Mutation, Truncation, and Temperature on the Folding Kinetics of a WW Domain. Journal Of Molecular Biology 420, 350-365.

Jiang, X. W., Zhong, A. H., Chen, C. J., Huang, Y. Z. & Xiao, Y. (2012). Network approach to identify the folding transition states of peptides and proteins. Physical Review E 86.

Gong, Z., Zhao, Y., Chen, C. & Xiao, Y. (2012). Computational study of unfolding and regulation mechanism of preQ1 riboswitches. PLoS One 7, e45239.

Chen, C., Huang, Y. & Xiao, Y. (2012). Free-energy calculations along a high-dimensional fragmented path with constrained dynamics. Phys Rev E Stat Nonlin Soft Matter Phys 86, 031901.


Zhou, R., He, Y. & Xiao, Y. (2011). Multi-nucleation and vectorial folding pathways of large helix protein. Computational Biology And Chemistry 35, 169-173.

Zhao, Y. J., Gong, Z. & Xiao, Y. (2011). Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. Journal Of Biomolecular Structure & Dynamics 28, 815-826.

Li, L., Guo, D. C., Huang, Y. Y., Liu, S. Y. & Xiao, Y. (2011). ASPDock: protein-protein docking algorithm using atomic solvation parameters model. Bmc Bioinformatics 12.

Lei, H. X., Chen, C. J., Xiao, Y. & Duan, Y. (2011). The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. Journal Of Chemical Physics 134.

Gong, Z., Zhao, Y. J., Chen, C. J. & Xiao, Y. (2011). Role of Ligand Binding in Structural Organization of Add A-riboswitch Aptamer: A Molecular Dynamics Simulation. Journal Of Biomolecular Structure & Dynamics 29, 403-416.

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Wang, G. Y., Du, C. H., Chen, H., Simha, R., Rong, Y. W., Xiao, Y. & Zeng, C. (2010). Process-based network decomposition reveals backbone motif structure. Proceedings Of the National Academy Of Sciences Of the United States Of America 107, 10478-10483.

Jiang, X. W., Chen, C. J. & Xiao, Y. (2010). Improvements of Network Approach for Analysis of the Folding Free-Energy Surface of Peptides and Proteins. Journal Of Computational Chemistry 31, 2502-2509.

Gong, Z., Zhao, Y. J. & Xiao, Y. (2010). RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models. Journal Of Biomolecular Structure & Dynamics 28, 431-441.

Feng, J. H., Li, M. F., Huang, Y. Z. & Xiao, Y. (2010). Symmetric Key Structural Residues in Symmetric Proteins with Beta-Trefoil Fold. Plos One 5.

Chen, C. J. & Xiao, Y. (2010). Accurate Free Energy Calculation along Optimized Paths. Journal Of Computational Chemistry 31, 1368-1375.


Xiao, Y., Chen, C. J. & He, Y. (2009). Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways. International Journal Of Molecular Sciences 10, 2838-2848.

Li, M., Huang, Y. & Xiao, Y. (2009). A method for identification of selenoprotein genes in archaeal genomes. Genomics Proteomics Bioinformatics 7, 62-70.

He, Y., Zhou, R., Huang, Y. & Xiao, Y. (2009). Foldable subunits of helix protein. Comput Biol Chem 33, 325-8.

He, Y., Xiao, Y., Liwo, A. & Scheraga, H. A. (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, 2127-35.

He, Y., Chen, C. & Xiao, Y. (2009). United-residue (UNRES) Langevin dynamics simulations of trpzip2 folding. J Comput Biol 16, 1719-30.

Chen, H., Huang, Y. & Xiao, Y. (2009). A simple method of identifying symmetric substructures of proteins. Comput Biol Chem 33, 100-7.


Wang, X., Huang, Y. & Xiao, Y. (2008). Structural-symmetry-related sequence patterns of the proteins of beta-propeller family. J Mol Graph Model 26, 829-33.

Li, M., Huang, Y. & Xiao, Y. (2008). Effects of external interactions on protein sequence-structure relations of beta-trefoil fold. Proteins 72, 1161-70.

Chen, C. & Xiao, Y. (2008). Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories. Bioinformatics 24, 659-65.


Ji, X., Chen, H. & Xiao, Y. (2007). Hidden symmetries in the primary sequences of beta-barrel family. Comput Biol Chem 31, 61-3.

Huang, Y. & Xiao, Y. (2007). Detection of gene duplication signals of Ig folds from their amino acid sequences. Proteins 68, 267-72.

Chen, C., Li, L. & Xiao, Y. (2007). All-atom contact potential approach to protein thermostability analysis. Biopolymers 85, 28-37.


Zhang, S. & Xiao, Y. (2006). Quasiperiodic property in Alu repeats. Phys Rev E Stat Nonlin Soft Matter Phys 74, 022901.

Chen, C. J., Li, L. & Xiao, Y. (2006). Identification of key residues in proteins by using their physical characters. Physical Review E 73.

Chen, C. & Xiao, Y. (2006). Molecular dynamics simulations of folding processes of a beta-hairpin in an implicit solvent. Phys Biol 3, 161-71.


Chen, C. J., Xiao, Y. & Zhang, L. S. (2005). A directed essential dynamics simulation of peptide folding. Biophysical Journal 88, 3276-3285.


Xiao, Y., Huang, Y. Z., Li, M. F., Xu, R. Z. & Xiao, S. F. (2003). Nonlinear analysis of correlations in Alu repeat sequences in DNA. Physical Review E 68.