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Huazhong University of Science and Technology

Huang Laboratary


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PUBLICATIONS
Papers and book chapters, etc.

Peer reviewed articles:

  1. Yan Y, Zhang D, Zhou P, Li B, Huang S-Y.* HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research 2017 (in press).

  2. Huang S-Y.* Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Brief Bioinform. 2017, doi: 10.1093/bib/bbx030.

  3. Yan Y, Wen Z, Wang X, Huang S-Y.* Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking. Proteins. 2017 Mar;85(3):497-512.

  4. Lensink MF, Velankar S, Kryshtafovych A, Huang S-Y, Schneidman-Duhovny D, …, Wodak SJ. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins: Structure Function, and Bioinformatics, DOI: 10.1002/prot.25007, 2016.

  5. Huang, S.-Y.*, Li, M., Wang, J., Pan, Y. HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein-and Ligand-Based Approaches. Journal of chemical information and modeling, 56: 1078–1087, 2016

  6. Huang, S.-Y.* Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking. Drug Discovery Today, 20: 969-977, 2015.

  7. Huang, S.-Y., Zou, X. A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Research, 42: e55, 2014.

  8. Lensink, M.F., Moal, I.H., …, Huang, S.-Y., Zou, X., ... Blind prediction of interfacial water positions in CAPRI. Proteins: Structure Function, and Bioinformatics, 82: 620-632, 2014.

  9. Huang, S.-Y.* Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discovery Today, 19: 1081-1096, 2014.

  10. Huang, S.-Y., Yan, C., Grinter, S.Z., Chang, S., Jiang, L., Zou X. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). Proteins: Structure Function, and Bioinformatics, 81: 2183-2191, 2013

  11. Huang, S.-Y.,* Springer, G.K. How the “Folding Funnel” Depends on Size and Structure of Proteins? A View from the Scoring Function Perspective. Tsinghua Science and Technology, 18: 462-468, 2013.

  12. Grinter, S.Z., Yan, C., Huang, S.-Y., Jiang, L., Zou, X. Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark. Journal of chemical information and modeling, 53: 1905-1914, 2013.

  13. Huang, S.-Y., Zou, X. ITScorePro – An efficient scoring program for evaluating the energy scores of protein structures. Methods in molecular biology (Clifton, NJ) 1137, 71-81, 2013.

  14. Moretti, R., Fleishman, S.J., …, Huang, S.-Y., Zou, X., ... Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins: Structure Function, and Bioinformatics, 81: 1980-1987, 2013.

  15. Huang, S.-Y., Zou, X. A nonredundant structure dataset for benchmarking protein-RNA computational docking. Journal of Computational Chemistry, 34: 311-318, 2013. [Cover Article]

  16. Huang, S.-Y., Zou, X. Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function. Journal of Chemical Information and Modeling, 51: 2097-2106, 2011.

  17. Huang, S.-Y., Zou, X. Construction and Test of Ligand Decoy Sets Using MDock: Community Structure Activity Resource Benchmarks for Binding Mode Prediction. Journal of Chemical Information and Modeling, 51: 2107-2114, 2011.

  18. Fleishman, S. J., Whitehead, T. A., …, Huang, S.-Y., Zou, X., Wodak, S. J., Janin, J., Baker, D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology, 414: 289-302, 2011.

  19. Huang, S.-Y., Zou, X. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures. Proteins: Structure Function, and Bioinformatics 79: 2648-2661, 2011.

  20. Rockey, W. M., Hernandez, F. J., Huang, S.-Y., Cao, S., et al. Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic acid therapeutics 21: 299-314, 2011.

  21. Grinter, S. Z., Liang, Y., Huang, S.-Y., Hyder, S. M., Zou, X. An inverse docking approach for identifying new potential anti-cancer targets. Journal of Molecular Graphics and Modelling 29:795-799, 2011

  22. Zhang, G., Huang, S.-Y., Yang, J., Shi, J., Yang, X., Moller, A., Zou, X., Cui, J. Ion sensing in the RCK1 domain of BK channels. Proceedings of National Academy of Sciences USA 107:18700-18705, 2010.

  23. Wang FH, TU YF, Sang JP, Huang SY, Zou XW, Aspect ratio-dependent optical properties of Ni-P/AAO nano-array composite structure. Journal of Material Science 45:3735-3740, 2010.

  24. Tu YF, Huang SY, Sang JP, Zou XW, Preparation of Fe-doped TiO2 nanotube arrays and their photocatalytic activities under visible light. Materials Research Bulletin 45:224-229, 2010.

  25. Huang, S.-Y., Zou, X. MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins: Structure Function, and Bioinformatics 78:3096-3103, 2010.

  26. Huang, S.-Y., Zou, X. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. Journal of Chemical Information and Modeling 50:262-273, 2010.

  27. Huang, S.-Y., Zou, X. Advances and challenges in protein-ligand docking. International Journal of Molecular Science 11:3016-3034, 2010.

  28. Huang, S.-Y., Grinter, S.Z., Zou, X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Physical Chemisty Chemical Physics 12:12899-908, 2010.

  29. Yu T, Zou XQ, Huang SY, Zou XW, Cutoff variation induces different topological properties: a new discovery of amino acid network within protein, Journal of Theoretical Biology 256,408-413, 2009.

  30. Tu YF, Huang SY, Sang JP, Zou XW, Synthesis and photocatalytic properties of Sn-doped TiO2 nanotube arrays. Journal of Alloys and Compounds 482,382-387, 2009.

  31. Liu YF, Wang FH, Guo DL, Huang SY, Sang JP, Zou XW, Effects of heat treatment on optical absorption properties of Ni-P/AAO nano-array composite structure. Applied Physics A 97,677-681, 2009.

  32. Liu YF, Tu YF, Huang SY, Sang JP, Zou XW, Effect of etch-treatment upon the intensity and peak position of photoluminescence spectra for anodic aluminum films with ordered nanopore array. Journal of Material Science 44, 3370-3375, 2009.

  33. Huang, S.-Y., Bolser, D., Liu, H.-Y., Hwang, T.-C., Zou, X. Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach. Journal of Molecular Graphics and Modelling 27: 822-828, 2009.

  34. Zhu XL, Zou XW, Shao ZG, Huang SY, and Sang JP. Homogeneity of load distribution plays a key role in global synchronizability of complex networks. Journal of Physical Society of Japan 77, 014001 2008.

  35. Zhu XL, Sang JP, Wang LL, Huang SY, Zou XW,. Structure and synchronizability of cobweb-like networks. Physica A 387, 6646-56, 2008.

  36. Zhang, L.Q., Adyshev, D.M., Singleton, P., Li, H., Cepeda, J., Huang, S.-Y., Zou, X., et al. Interactions between PBEF and oxidative stress proteins - A potential new mechanism underlying PBEF in the pathogenesis of acute lung injury. FEBS Letters 582:1802-1808, 2008.

  37. Tu YF, Wei RB, Sang JP, Huang SY, Zou XW. Alternating morphology transitions in crystallization of NH4Cl on agar plates. Physical Revew E 77, 041601, 2008.

  38. Tu YF, Chao XH, Sang JP, Huang SY, Zou XW. Thin-layer electrodeposition of Zn in the agar gel medium. Physica A 387, 4007, 2008.

  39. Jia SF, Tu YF, Wei RB, Huang SY, Sang JP, Zou XW, Microstructure, composition analysis and formation mechanism of Pb-Sn multilayered film synthesized by thin layer electrochemical deposition. Materials Science and Technology 24, 947-980, 2008.

  40. Huang, S.-Y., Zou, X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins: Structure Function, and Bioinformatics 72: 557-579, 2008.

  41. Guo DL, Fan LX, Sang JP, Wang FH, Huang SY, Zou XW, Porous Anodic Aluminum Oxide Bragg Stacks as Chemical Sensors. Journal of Chemical Physics 112, 17952-17956, 2008.

  42. Huang, S.-Y., Zou, X. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking. Proteins: Structure Function, and Bioinformatics 66: 399-421, 2007.

  43. Huang, S.-Y., Zou, X. Efficient molecular docking of NMR structures: Application to HIV-1 protease. Protein Science 16:43-51, 2007.

  44. Zou XW, Dong SX, and Huang SY. Effect of residue mutation on the electrostatic potential in EcClC. Journal of Wuhan University (Nat Sci Ed) 12, 1029-1033, 2007.

  45. Zhang W, Huang SY, Yu T, Zou X, Investigation of highly designable dented structures in HP model with hydrogen bond energy, Journal of Wuhan University (Nat Sci Ed) 12, 1034-1038, 2007.

  46. Yu T, Sun ZB, Sang JP, Huang SY, Zou XW, Structural class tendency of polypeptide: a new conception in predicting protein structural class, Physica A 386, 581-589, 2007.

  47. Guo DL, Fan LX, Sang JP, Liu YF, Huang SY, Zou XW, Fabrication of a regular tripod Ni-P nanorod array and an AAO template with regular branched nanopores using a current-controlled branching method. Nanotechnology 18, 405304, 2007.

  48. Huang, S.-Y., Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. Journal of Computational Chemistry 27:1876-1882, 2006.

  49. Huang, S.-Y., Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. Journal of Computational Chemistry 27:1866-1875, 2006.

  50. Gatto, C., Helms, J. B., Prasse, M. C., Huang, S.-Y., Zou, X., Arnett, K. L., Milanick, M. A. Similarities and differences between organic cation inhibition of the Na,K-ATPase and PMCA. Biochemistry 45:13331-13345, 2006.

  51. Shao, Z.-G., Zou, X.-W., Tan, Z.-J., Huang, S.-Y., Jin, Z.-Z. Deposition, diffusion, and aggregation on small-world networks: a model for nanostructure growth on the defective substrate. Physics Letters A 331: 105-109, 2004.

  52. Huang, S.-Y., Zou, X.-W., Shao, Z.-G., Tan, Z.-J., Jin, Z.-Z. Particle-cluster aggregation on a small-world network. Physical Review E 69: 067104(1-4), 2004.

  53. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Shao, Z.-G., Jin, Z.-Z. Critical behavior of efficiency dynamics in small-world networks. Physical Review E 68: 016107(1-6), 2003.

  54. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Network-induced nonequilibrium phase transition in the "game of Life". Physical Review E 67: 026107(1-6), 2003.

  55. Tan, Z.-J., Zou, X.-W., Zhang, W., Huang, S.-Y., Jin, Z.-Z. Self-attracting walk on nonuniform substrates. Modern Physics Letters B 16:449-457, 2002.

  56. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Zhang, W., Jin, Z.-Z. Patterns of particle distribution in multiparticle systems by random walks with memory enhancement and decay. Physical Review E 66:011101(1-5), 2002.

  57. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Jin, Z.-Z. Random walk with memory enhancement and decay. Physical Review E 65:041101(1-5), 2002.

  58. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Jin, Z.-Z. Particle-cluster aggregation with repulsive interactions on nonuniform substrates. Physics Letters A 297:242-246, 2002.

  59. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Jin, Z.-Z. Deposition, diffusion, and aggregation on Leath percolation: A model for nanostructure growth on nonuniform substrate. Physical Review B 65:235403(1-5), 2002.

  60. Huang, S.-Y., Zou, X.-W., Zhang, W.-B., Jin, Z.-Z. Random walk on a (2+1)-dimensional deformable medium. Physical Review Letters 88:056102(1-4), 2002.

  61. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Short-time critical dynamics in two-dimensional vapor-liquid transition. Physics Letters A 297:105-109, 2002.

  62. Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Multiparticle random walks on a deformable medium. Physical Review E 66:041112(1-8), 2002.

  63. Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Directed random walks in continuous space. Physical Review E 65:052105(1-4), 2002.

  64. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Jin, Z.-Z. Diffusion-limited aggregation on nonuniform substrates. Journal of the Physical Society of Japan 70:3251-3254, 2001.

  65. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Particle-cluster aggregation by randomness and directive correlation of particle motion. Physics Letters A 292:141-145, 2001.

  66. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Influence of the long-range interaction on the energy localization in 1D chain with an impurity. Physica A 296:426-436, 2001.

  67. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Early dynamics of the potential energy evolution in two-dimensional gas-liquid phase transition. Journal of Physics: Condensed Matter 13:7343-7352, 2001.

  68. Huang, S.-Y., Zou, X.-W., Tan, Z.-J., Jin, Z.-Z. Determination of the vapor-liquid critical point from the short-time dynamics. Modern Physics Letters B 15:369-374, 2001.

  69. Huang, S.-Y., Zou, X.-W., Zhang, W.-B., Jin, Z.-Z. Molecular dynamics simulation of the energy localization of an impurity solved in 1D lattice. Physica A 284:231-240, 2000.

  70. Huang, S.-Y., Zou, X.-W., Zhang, W.-B., Jin, Z.-Z. Influence of repulsive and attractive potentials on the energy localization in 1D Morse lattice with an impurity. Journal of the Physical Society of Japan 69:2900-2904, 2000.

  71. Huang, S.-Y., Zhang, W.-B., D. Ren, Jin, Z.-Z., Zou, X.-W. Local energy excitation in one-dimension-chain with an impurity molecule. Journal of Wuhan University (Nature Science Edition) 45:347-350, 1999.

Book chapters:

  1. Huang, S.-Y., Zou, X. Mean-force scoring functions for protein-ligand binding. Annual Report in Computational Chemistry , vol. 6, pp. 280-296, Edited by: R. A. Wheeler (Elsevier Ltd., 2010).

  2. Huang, S.-Y., Zhang, W.-B., Zou, X.-W., Diffusion of a particle on a deformable plane. in Progress in Liquid Physics (2001), pp.107-110, edited by K.-Q. Lu, and H.-R Ma, (Shanghai Jiaotong University Press, Shanghai, 2001).

  3. Zhang, W.-B., Zou, X.-W., H. Liu, S. Zhang, H. Li, Huang, S.-Y., Dynamic heterogeneous structure relaxation of supercooled liquid. in Progress in Liquid Physics (II) , pp.111-115, edited by K.-Q Lu, and X.-W. Zou, (Wuhan University Press, Wuhan, 2000).


huanglab@hust.edu.cn, Lab of Biophysics and Molecular Modeling