Biomolecular Physics and Modeling Group
  • 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.

  • Miao, Z., R. W. Adamiak, M. Antczak, R. T. Batey, A. J. Becka, M. Biesiada, M. J. Boniecki, J. M. Bujnicki, S. J. Chen, C. Y. Cheng, F. C. Chou, A. R. Ferre-D'Amare, R. Das, W. K. Dawson, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, K. Kappel, W. Kladwang, A. Krokhotin, G. E. Lach, F. Major, T. H. Mann, M. Magnus, K. Pachulska-Wieczorek, D. J. Patel, J. A. Piccirilli, M. Popenda, K. J. Purzycka, A. Ren, G. M. Rice, J. Santalucia, Jr., J. Sarzynska, M. Szachniuk, A. Tandon, J. J. Trausch, S. Tian, J. Wang, K. M. Weeks, B. Williams, 2nd, Y. Xiao, X. Xu, D. Zhang, T. Zok and E. Westhof (2017). "RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme." RNA 23(5): 655-672.

  • Li, H., Y. Huang and Y. Xiao (2017). "A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures." PLoS One 12(3): e0174662.

  • Ji, X., Y. Xiao and S. Liu (2017). "Structural modeling of human cardiac sodium channel pore domain." J Biomol Struct Dyn: 1-11.

  • Wang, J. and Y. Xiao (2016). "Types and concentrations of metal ions affect local structure and dynamics of RNA." Phys Rev E 94(4-1): 040401.

  • Huang, Y., H. Li and Y. Xiao (2016). "Using 3dRPC for RNA-protein complex structure prediction." Biophys Rep 2(5): 95-99.

  • 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.

  • Miao, Z., R. W. Adamiak, M. F. Blanchet, M. Boniecki, J. M. Bujnicki, S. J. Chen, C. Cheng, G. Chojnowski, F. C. Chou, P. Cordero, J. A. Cruz, A. R. Ferre-D'Amare, R. Das, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, W. Kladwang, A. Krokhotin, G. Lach, M. Magnus, F. Major, T. H. Mann, B. Masquida, D. Matelska, M. Meyer, A. Peselis, M. Popenda, K. J. Purzycka, A. Serganov, J. Stasiewicz, M. Szachniuk, A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, T. Zok and E. Westhof (2015). "RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures." RNA 21(6): 1066-1084.

  • Chen, C., Y. Xiao and Y. Huang (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.

  • Gong, Z., Y. Zhao, C. Chen, Y. Duan and Y. Xiao (2014). "Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations." PLoS One 9(3): e92247.

  • Chen, C., Y. Huang, X. Jiang and Y. Xiao (2014). "A fast tomographic method for searching the minimum free energy path." J Chem Phys 141(15): 154109.

  • 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 Sci 56(10): 953-959.

  • 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.

  • Guo, D., S. Liu, Y. Huang and Y. Xiao (2013). "Preorientation of protein and RNA just before contacting." J Biomol Struct Dyn 31(7): 716-728.

  • 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.

  • Chen, C., Y. Huang and Y. Xiao (2013). "Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath." J Biomol Struct Dyn 31(2): 206-214.

  • Chen, C., Y. Huang, X. Jiang and Y. Xiao (2013). "Binding free-energy calculation of an ion-peptide complex by constrained dynamics." Phys Rev E Stat Nonlin Soft Matter Phys 87(6): 062705.

  • Chen, C., Y. Huang, X. Ji and Y. Xiao (2013). "Efficiently finding the minimum free energy path from steepest descent path." J Chem Phys 138(16): 164122.

  • 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.

  • Wu, D., H. Li, W. Du, X. Ji, W. Liu, S. Huang and Y. Xiao (2012). "Mathematical modeling of therapeutic strategies for myeloid malignancies." Pathol Oncol Res 18(4): 939-947.

  • Maisuradze, G. G., R. Zhou, A. Liwo, Y. Xiao and H. A. Scheraga (2012). "Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain." J Mol Biol 420(4-5): 350-365.

  • Jiang, X., A. Zhong, C. Chen, Y. Huang and Y. Xiao (2012). "Network approach to identify the folding transition states of peptides and proteins." Phys Rev E Stat Nonlin Soft Matter Phys 86(5 Pt 1): 051901.

  • Guo, D., S. Liu, Y. Huang and Y. Xiao (2012). "Preorientation of protein and RNA just before contacting." J Biomol Struct Dyn.

  • 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.

  • Chen, C., Y. Huang and Y. Xiao (2012). "Free-energy calculations along a high-dimensional fragmented path with constrained dynamics." Phys Rev E Stat Nonlin Soft Matter Phys 86(3 Pt 1): 031901.

  • Zhou, R., Y. He and Y. Xiao (2011). "Multi-nucleation and vectorial folding pathways of large helix protein." Comput Biol Chem 35(3): 169-173.

  • Zhao, Y., Z. Gong and Y. Xiao (2011). "Improvements of the hierarchical approach for predicting RNA tertiary structure." J Biomol Struct Dyn 28(5): 815-826.

  • Li, L., D. Guo, Y. Huang, S. Liu and Y. Xiao (2011). "ASPDock: protein-protein docking algorithm using atomic solvation parameters model." BMC Bioinformatics 12: 36.

  • Lei, H., C. Chen, Y. Xiao and Y. Duan (2011). "The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel." J Chem Phys 134(20): 205104.

  • Gong, Z., Y. Zhao, C. Chen and Y. Xiao (2011). "Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation." J Biomol Struct Dyn 29(2): 403-416.

  • Fleishman, S. J., T. A. Whitehead, E. M. Strauch, J. E. Corn, S. Qin, H. X. Zhou, J. C. Mitchell, O. N. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J. S. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Aze, S. Soner, S. K. Ovali, P. Ozbek, N. B. Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Perez-Cano, C. Pons, J. Fernandez-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li, D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Potapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M. Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodriguez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S. Y. Huang, X. Zou, S. J. Wodak, J. Janin and D. Baker (2011). "Community-wide assessment of protein-interface modeling suggests improvements to design methodology." J Mol Biol 414(2): 289-302.

  • 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.

  • Jiang, X., C. Chen and Y. Xiao (2010). "Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins." J Comput Chem 31(13): 2502-2509.

  • Gong, Z., Y. Zhao and Y. Xiao (2010). "RNA stability under different combinations of amber force fields and solvation models." J Biomol Struct Dyn 28(3): 431-441.

  • Feng, J., M. Li, Y. Huang and Y. Xiao (2010). "Symmetric key structural residues in symmetric proteins with beta-trefoil fold." PLoS One 5(11): e14138.

  • Chen, C. and Y. Xiao (2010). "Accurate free energy calculation along optimized paths." J Comput Chem 31(7): 1368-1375.

  • 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.

  • Li, M., Y. Huang and Y. Xiao (2009). "A method for identification of selenoprotein genes in archaeal genomes." Genomics Proteomics Bioinformatics 7(1-2): 62-70.

  • He, Y., R. Zhou, Y. Huang and Y. Xiao (2009). "Foldable subunits of helix protein." Comput Biol Chem 33(4): 325-328.

  • 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.

  • He, Y., C. Chen and Y. Xiao (2009). "United-residue (UNRES) Langevin dynamics simulations of trpzip2 folding." J Comput Biol 16(12): 1719-1730.

  • Chen, H., Y. Huang and Y. Xiao (2009). "A simple method of identifying symmetric substructures of proteins." Comput Biol Chem 33(1): 100-107.

  • Wang, X., Y. Huang and Y. Xiao (2008). "Structural-symmetry-related sequence patterns of the proteins of beta-propeller family." J Mol Graph Model 26(5): 829-833.

  • 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.

  • Ji, X., H. Chen and Y. Xiao (2007). "Hidden symmetries in the primary sequences of beta-barrel family." Comput Biol Chem 31(1): 61-63.

  • Huang, Y. and Y. Xiao (2007). "Detection of gene duplication signals of Ig folds from their amino acid sequences." Proteins 68(1): 267-272.

  • Chen, C., L. Li and Y. Xiao (2007). "All-atom contact potential approach to protein thermostability analysis." Biopolymers 85(1): 28-37.

  • 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. and Y. Xiao (2006). "Molecular dynamics simulations of folding processes of a beta-hairpin in an implicit solvent." Phys Biol 3(3): 161-171.

  • Chen, C., L. Li and Y. Xiao (2006). "Identification of key residues in proteins by using their physical characters." Phys Rev E Stat Nonlin Soft Matter Phys 73(4 Pt 1): 041926.

  • Zhang, M., C. Chen, Y. He and Y. Xiao (2005). "Improvement on a simplified model for protein folding simulation." Phys Rev E Stat Nonlin Soft Matter Phys 72(5 Pt 1): 051919.

  • Xu, R. and Y. Xiao (2005). "A common sequence-associated physicochemical feature for proteins of beta-trefoil family." Comput Biol Chem 29(1): 79-82.

  • Chen, C., Y. Xiao and L. Zhang (2005). "A directed essential dynamics simulation of peptide folding." Biophys J 88(5): 3276-3285.

  • Xiao, Y., Y. Huang, M. Li, R. Xu and S. Xiao (2003). "Nonlinear analysis of correlations in Alu repeat sequences in DNA." Phys Rev E Stat Nonlin Soft Matter Phys 68(6 Pt 1): 061913.

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