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Huazhong University of Science and Technology

Huang Laboratory


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PUBLICATIONS
Papers and book chapters, etc.

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

• Selected papers:

  1. Li T, He J, Cao H, Zhang Y, Chen J, Xiao Y*, Huang S-Y*. All-atom RNA structure determination from cryo-EM maps. Nature Biotechnology, 2024, [link] [pdf] [Software]

  2. Lin P, Tao H, Li H, Huang S-Y.* Protein-protein contact prediction by geometric triangle-aware protein language models. Nature Machine Intelligence, 2023;5:1275–1284. [link] [pdf] [Software]

  3. Lin P, Yan Y, Tao H, Huang S-Y.* Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes. Nature Communications, 2023;14:4935. [link] [Software]

  4. He J, Li T, Huang S-Y.* Improvement of cryo-EM maps by simultaneous local and non-local deep learning. Nature Communications, 2023;14:3217. [link] [Software]

  5. He J, Lin P, Chen J, Cao H, Huang S-Y.* Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. Nature Communications, 2022;13:4066. [link] [Software]

  6. Lei E,# Tao H,# Jiao S,# Yang A, Zhou Y, Wang M, Wen K, Wang Y, Chen Z, Chen X, Song J, Zhou C, Huang W, Xu L, Guan D, Tan C, Liu H, Cai Q, Zhou K, Modica J, Huang S-Y,* Huang W,* Feng X.* Potentiation of Vancomycin: Creating Cooperative Membrane Lysis through a "Derivatization-for-Sensitization" Approach. Journal of the American Chemical Society, 2022;144(23):10622-10639. link

  7. Yan Y,# Tao H,# He J, Huang S-Y.* The HDOCK server for integrated protein-protein docking. Nature Protocols, 15: 1829-1852, 2020. [link] [Software]

  8. He J,# Wang J,# Tao H, Xiao Y*, Huang S-Y.* HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. Nucleic Acids Research, 47: W35-W42, 2019. [Online] [Server]

  9. 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

  10. 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

  11. 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

  12. 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

• All publications:

    2024
  1. Li T, He J, Cao H, Zhang Y, Chen J, Xiao Y*, Huang S-Y*. All-atom RNA structure determination from cryo-EM maps. Nature Biotechnology, 2024, [link] [pdf] [Software]

  2. Lin P, Li H, Huang S-Y*. Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches. Current Opinion in Structural Biology, 2024, 85:102789. [pdf].

    3. 2023
  3. Lin P, Tao H, Li H, Huang S-Y.* Protein-protein contact prediction by geometric triangle-aware protein language models. Nature Machine Intelligence, 2023;5:1275–1284. [link] [pdf] [Software]

  4. Zhao X, Li H, Zhang K, Huang S-Y.* Iterative Knowledge-Based Scoring Function for Protein-Ligand Interactions by Considering Binding Affinity Information. Journal of the Physical Chemistry B, 2023, doi: 10.1021/acs.jpcb.3c04421.[link] [Software]

  5. Lin P, Yan Y, Tao H, Huang S-Y.* Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes. Nature Communications, 2023;14:4935. [link] [Software]

  6. He J, Li T, Huang S-Y.* Improvement of cryo-EM maps by simultaneous local and non-local deep learning. Nature Communications, 2023;14:3217. [link] [Software]

  7. Wu Q, Huang S-Y.* HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. Briefings in Bioinformatics, 2023;24(1):bbac559. [link] [Software]

    8. 2022
  8. He J, Lin P, Chen J, Cao H, Huang S-Y.* Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. Nature Communications, 2022;13:4066. [link] [Software]

  9. Lei E,# Tao H,# Jiao S,# Yang A, Zhou Y, Wang M, Wen K, Wang Y, Chen Z, Chen X, Song J, Zhou C, Huang W, Xu L, Guan D, Tan C, Liu H, Cai Q, Zhou K, Modica J, Huang S-Y,* Huang W,* Feng X.* Potentiation of Vancomycin: Creating Cooperative Membrane Lysis through a "Derivatization-for-Sensitization" Approach. Journal of the American Chemical Society, 2022;144(23):10622-10639. link

  10. Tao H, Zhao X, Zhang K, Lin P, Huang S-Y.* Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. Bioinformatics, 2022;38(17):4109-4116. link

  11. Lin P, Yan Y, Huang S-Y.* DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Briefings in Bioinformatics, 2022:bbac499. [link] [Software]

  12. Zhang J, Li H, Zhao X, Wu Q, Huang S-Y.* Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. Journal of Chemical Information and Modeling, 2022;62(22):5806-5820. link

  13. Li H, Huang E, Zhang Y, Huang S-Y,* Xiao Y.* HDOCK update for modeling protein-RNA/DNA complex structures. Protein Science, 2022;31(11):e4441. [link] [Server]

  14. Tao H, Wu Q, Zhao X, Lin P, Huang S-Y.* Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. Journal of Cheminformatics, 2022;14(1):26. [link] [Software]

  15. Guo L,# He J,# Lin P, Huang S-Y,* Wang J.* TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics, 2022: btac120. link

  16. Yang A, Tao H, Szymczak LC, Lin L, Song J, Wang Y, Bai S, Modica J, Huang S-Y,* Mrksich M,* Feng X.* Efficient Enzymatic Incorporation of Dehydroalanine Based on SAMDI-Assisted Identification of Optimized Tags for OspF/SpvC. ACS Chemical Biology, 2022; 17(2):414-425. link

  17. Li H, Yan Y, Zhao X, Huang S-Y.* Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. Journal of Chemical Information and Modeling, 2022; 62(3):740-750.link

  18. Feng Y, Yan Y, He J, Tao H, Wu Q, Huang S-Y.* Docking and scoring for nucleic acid-ligand interactions: Principles and current status. Drug Discovery Today, 2022; 27(3):838-847. link

    19. 2021
  19. Hu F, Song D, Yan Y, Huang C, Shen C, Lan J, Cheng Y, Liu A, Wu Q, Sun L, Xu F, Hu F, Chen L, Luo X, Feng Y, Huang S-Y, Hu J,* Wang G.* IL-6 regulates autophagy and chemotherapy resistance by promoting BECN1 phosphorylation. Nature Communications, 12(1):3651, 2021. link

  20. He J, Huang S-Y.,* Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinformatics, 2021;37(20):3480–3490. [link] [Software]

  21. Feng Y, Zhang K, Wu Q, Huang S-Y.* NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. Journal of Chemical Information and Modeling, 2021;61(9):4771-4782. [link] [Software]

  22. He J, Huang S-Y.* EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. Briefings in Bioinformatics, 2021;22(6):bbab156. [link] [Software]

  23. Lensink MF, ..., Yan Y, Li H, Lin P, Huang S-Y, ..., Wodak SJ. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins, 2021;89(12):1800-1823. link

  24. Yan Y, Huang S-Y.* Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes. Briefings in Bioinformatics, 2021;22(5):bbab038. [link] [Software]

  25. Ma Z, Huang S-Y, Cheng F, Zou X.* Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases. The Journal of Physical Chemistry B, 125: 2288-2298, 2021. link

  26. Li H, Huang S-Y.* Protein-protein docking with interface residue restraints. Chinese Physics B, 30: 018703, 2021. link

  27. Huang D, Tao H, Wu Q, Huang S-Y,* Xiao Y.* Modeling of the Long-Term Epidemic Dynamics of COVID-19 in the United States. Int J Environ Res Public Health, 2021;18(14):7594. link

    28. 2020
  28. Yan Y,# Tao H,# He J, Huang S-Y.* The HDOCK server for integrated protein-protein docking. Nature Protocols, 15: 1829-1852, 2020. [link] [Software]

  29. Wen Z, He J, Huang S-Y.* Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinformatics, 36: 478-486, 2020. link

  30. He J, Tao H, Yan Y, Huang S-Y.*, Xiao Y.* Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2. Viruses, 12: 428, 2020 link

  31. Feng Y, Huang S-Y. ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. Journal of Chemical Information and Modeling, 60(12):6698-6708, 2020. [link] [Software]

  32. Tao H,# Zhang Y,# Huang S-Y.* Improving Protein-Peptide Docking Results via Pose Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. Journal of Chemical Information and Modeling, 60: 2377-2387, 2020. link

  33. Yan Y, He J, Feng Y, Lin P, Tao H, Huang S-Y.* Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46. Proteins: Structure Function, and Bioinformatics, 88: 1055-1069, 2020. link

  34. Yan Y, Huang, S-Y.* Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver. Methods in molecular biology, 2165: 217-229, 2020. link

    35. 2019

  35. Yan Y, Huang S-Y.* Pushing the accuracy limit of shape complementarity for protein-protein docking. BMC Bioinformatics, 20: 696, 2019. link

  36. He J,# Wang J,# Tao H, Xiao Y*, Huang S-Y.* HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. Nucleic Acids Research, 47: W35-W42, 2019. [Online] [Server]

  37. He J, Tao H, Huang S-Y.* Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinformatics, 35: 4994-5002, 2019. link

  38. Wen Z, He J, Tao H, Huang S-Y.* PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinformatics, 35: 175-177, 2019. link

  39. Zhang Y, Huang S-Y.* Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA. Int J Mol Sci, 20: 5142, 2019 link

  40. Zhang Y, Tao H, Huang S-Y.* Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1. Int J Mol Sci, 20: 3325, 2019. link

  41. Wang X, Huang S-Y.* Integrating bonded and nonbonded potentials in the knowledge-based scoring function for protein structure prediction. Journal of Chemical Information and Modeling, 59: 3080-3090, 2019. link

  42. Yan Y, Huang S-Y.* A non-redundant benchmark for symmetric protein docking. Big Data Mining and Analytics, 2: 92-99, 2019. link

  43. Yan Y, Huang S-Y.* CHDOCK: a hierarchical docking approach for modeling Cn symmetric homo-oligomeric complexes. Biophysics Reports, 5: 65-72, 2019. link

    44. 2018

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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

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

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

    52. 2017

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

  53. 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

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

  55. 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

    56. 2016

  56. 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

  57. 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

    58. 2015

  58. 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

    59. 2014

  59. 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

  60. 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

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

    62. 2013

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

    68. 2011

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

    74. 2010

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

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

  80. 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

    81. 2009

  81. 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

  82. 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

  83. 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

  84. 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

  85. 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

    86. 2008

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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

    94. 2007

  94. 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

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

  96. 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

  97. 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

  98. 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

  99. 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

    100. 2006

  100. 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

  101. 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

  102. 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

    103. 2004

  103. 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

  104. 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

    105. 2003

  105. 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

  106. 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

    107. 2002

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

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

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

    116. 2001

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

    121. 2000

  121. 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

  122. 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

    123. 1999

  123. 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).

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