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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:

    Google Scholar Citations:  https://scholar.google.com/citations?user=aQg2lRoAAAAJ&hl=en

    2018

  1. Wen Z, He J, Tao H, Huang S-Y.* PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinformatics, doi: 10.1093/bioinformatics/bty579, 2018 (in press). link

  2. Yan Y, Huang S-Y.* Protein-Protein Docking with Improved Shape Complementarity. International Conference on Intelligent Computing, 600-605, 2018. link

  3. Zhou P, Jin B, Li H, Huang S-Y.* HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, 46: W443-W450, 2018. link

  4. Yan Y, Tao H, Huang S-Y.* HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. Nucleic Acids Research, 46: W443-W450, 2018. link

  5. Zhou P, Li B, Yan Y, Jin B, Wang L, Huang S-Y.* Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. Journal of Chemical Information and Modeling, 58: 1292-1302, 2018. link

  6. Yan Y,# Wen Z,# Zhang D, Huang S-Y.* Determination of an effective scoring function for RNA–RNA interactions with a physics-based double-iterative method. Nucleic Acids Research, 46: e56, 2018. link

  7. Wang X, Zhang D, Huang S-Y.* New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. Journal of Chemical Information and Modeling, 58: 724-732, 2018. link

  8. Wang X, Huang S-Y.* Optimizing the atom types of proteins through iterative knowledge-based potentials. Chinese Physics B, 27: 20503-020503, 2018. link

  9. Yan Y, Huang S-Y.* RRDB: A comprehensive and nonredundant benchmark for RNA-RNA docking and scoring. Bioinformatics, 34: 453-458, 2018. link

    10. 2017

  10. Yan Y, Zhang D, Huang S-Y.* Efficient conformational ensemble generation of protein-bound peptides. Journal of Cheminformatics, 9: 59, 2017. link

  11. 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, 45: W365-373, 2017. link

  12. Huang S-Y.* Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Briefings in Bioinformatics, 19: 982-994, 2017. link

  13. 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: Structure Function, and Bioinformatics, 85: 497-512, 2017. link

    14. 2016

  14. 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, 84: 323-348, 2016. link

  15. 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. link

    16. 2015

  16. 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. link

    17. 2014

  17. 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. link

  18. 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. link

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

    20. 2013

  20. 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. link

  21. 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. link

  22. 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. link

  23. 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. link

  24. 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. link

  25. 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] link

    26. 2011

  26. 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. link

  27. 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. link

  28. 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. link

  29. 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. link

  30. 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. link

  31. 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. link

    32. 2010

  32. 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. link

  33. 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. link

  34. 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. link

  35. 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. link

  36. 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. link

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

  38. 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. link

    39. 2009

  39. 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. link

  40. 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. link

  41. 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. link

  42. 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. link

  43. 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. link

    44. 2008

  44. 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. link

  45. Zhu XL, Sang JP, Wang LL, Huang SY, Zou XW,. Structure and synchronizability of cobweb-like networks. Physica A: Statistical Mechanics and its Applications, 387: 6646-56, 2008. link

  46. 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. link

  47. 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. link

  48. Tu YF, Chao XH, Sang JP, Huang SY, Zou XW. Thin-layer electrodeposition of Zn in the agar gel medium. Physica A: Statistical Mechanics and its Applications, 387: 4007, 2008. link

  49. 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. link

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

  51. 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. link

    52. 2007

  52. 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. link

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

  54. 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. link

  55. 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. link

  56. 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: Statistical Mechanics and its Application, 386: 581-589, 2007. link

  57. 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. link

    58. 2006

  58. 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. link

  59. 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. link

  60. 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. link

    61. 2004

  61. 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. link

  62. 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, 2004. link

    63. 2003

  63. 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, 2003. link

  64. 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, 2003. link

    65. 2002

  65. 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. link

  66. 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, 2002. link

  67. Tan, Z.-J., Zou, X.-W., Huang, S.-Y., Jin, Z.-Z. Random walk with memory enhancement and decay. Physical Review E, 65: 041101, 2002. link

  68. 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. link

  69. 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, 2002. link

  70. 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, 2002. link

  71. 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. link

  72. Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Multiparticle random walks on a deformable medium. Physical Review E, 66: 041112, 2002. link

  73. Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Directed random walks in continuous space. Physical Review E, 65: 052105, 2002. link

    74. 2001

  74. 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. link

  75. 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. link

  76. 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: Statistical Mechanics and its Applications, 296: 426-436, 2001. link

  77. 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. link

  78. 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. link

    79. 2000

  79. 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: Statistical Mechanics and its Applications, 284: 231-240, 2000. link

  80. 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. link

    81. 1999

  81. 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). link

  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 Bioinformatics and Molecular Modeling