Biomolecular Physics and Modeling Group
2015

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

2014

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.

2013

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.

2012

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.

2011

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.

Fleishman, S. J., Whitehead, T. A., Strauch, E. M., Corn, J. E., Qin, S. B., Zhou, H. X., Mitchell, J. C., Demerdash, O. N. A., Takeda-Shitaka, M., Terashi, G., Moal, I. H., Li, X. F., Bates, P. A., Zacharias, M., Park, H., Ko, J. S., Lee, H., Seok, C., Bourquard, T., Bernauer, J., Poupon, A., Aze, J., Soner, S., Ovali, S. K., Ozbek, P., Ben Tal, N., Haliloglu, T., Hwang, H., Vreven, T., Pierce, B. G., Weng, Z. P., Perez-Cano, L., Pons, C., Fernandez-Recio, J., Jiang, F., Yang, F., Gong, X. Q., Cao, L. B., Xu, X. J., Liu, B., Wang, P. W., Li, C. H., Wang, C. X., Robert, C. H., Guharoy, M., Liu, S. Y., Huang, Y. Y., Li, L., Guo, D. C., Chen, Y., Xiao, Y., London, N., Itzhaki, Z., Schueler-Furman, O., Inbar, Y., Potapov, V., Cohen, M., Schreiber, G., Tsuchiya, Y., Kanamori, E., Standley, D. M., Nakamura, H., Kinoshita, K., Driggers, C. M., Hall, R. G., Morgan, J. L., Hsu, V. L., Zhan, J., Yang, Y. D., Zhou, Y. Q., Kastritis, P. L., Bonvin, A. M. J. J., Zhang, W. Y., Camacho, C. J., Kilambi, K. P., Sircar, A., Gray, J. J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, Y., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodriguez, J., Kihara, D., Stranges, P. B., Jacak, R., Kuhlman, B., Huang, S. Y., Zou, X. Q., Wodak, S. J., Janin, J. & Baker, D. (2011). Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology. Journal Of Molecular Biology 414, 289-302.

2010

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.

2009

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.

2008

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.

2007

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.

2006

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.

2005

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

2003

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.

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