Academic Areas: Computational Biophysics, Bioinformatics, Molecular docking, Computer-aided drug design
Research Interests: Molecular modeling, bioinformatics, computational biophysics/biology and their application to drug discovery
Dr. Huang received his B.S. degree in Material Physics and his Ph.D. degree in Computational Soft Matter Physics from Wuhan University, Wuhan, China, in 2003. He is now a full professor in the School of Physics at Huazhong University of Science and Technology (HUST), Wuhan, China. Before joining the University, He was a research assistant professor at University of Missouri-Columbia, USA. He undertook postdoctoral research in molecular modeling and computational biophysics/biology at University of Missouri-Columbia. His research interests include molecular modeling, bioinformatics, computational biophysics/biology and their application to drug discovery. He actively develops novel docking algorithms and energy-scoring functions for protein–ligand interactions, protein–protein interactions, protein–RNA interactions, and modeling of quantitative structure-function relationships of therapeutically important proteins. His research has resulted in the publication of scientific software, book chapters and more than 70 peer-reviewed journal articles with more than 1300 citations from other scientists.
PhD in Computational Soft Matter Physics, 2003, Wuhan University
BS in Material Physics, 1998, Wuhan University
2015-present : Professor, Huazhong University of Science and Technology;
2011-2015: Research Assistant Professor, University of Missouri-Columbia;
2008-2011: Research Associate, University of Missouri-Columbia;
2003-2008: Postdoctoral Researcher, University of Missouri-Columbia.
Huang, S.-Y., Li, M., Wang, J., Pan, Y. Yi，HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.，Journal of Chemical Information and Modeling，DOI:10.1021/acs.jcim, 2015。
Huang, S.-Y. Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discovery Today, 20: 969-977，2015.
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.
Lensink, M.F., Moal, I.H., …, Huang, S.-Y., Zou, X., ... Blind prediction of interfacial water positions in CAPRI. Proteins, 82: 620-632, 2014.
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, 81: 2183-2191, 2013.
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.
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.
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, 81: 1980-1987, 2013.
Huang, S.-Y., Zou, X. A nonredundant structure dataset for benchmarking protein-RNA computational docking. Journal of Computational Chemistry, 34: 311-318, 2013.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Huang, S.-Y., Zou, X. Advances and challenges in protein-ligand docking. International Journal of Molecular Science 11:3016-3034, 2010.
Huang, S.-Y., Grinter, S.Z., Zou, X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Physical Chemistry Chemical Physics 12:12899-908, 2010.
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.
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.
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.
Huang, S.-Y., Zou, X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins: Structure Function, and Bioinformatics 72: 557-579, 2008.
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.
Huang, S.-Y., Zou, X. Efficient molecular docking of NMR structures: Application to HIV-1 protease. Protein Science 16:43-51, 2007.
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.
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.
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.
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.
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.
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.
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.
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.
Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Multiparticle random walks on a deformable medium. Physical Review E 66:041112(1-8), 2002.
Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Directed random walks in continuous space. Physical Review E 65:052105(1-4), 2002.
• 2015 “1000 Young Talent Program” of P.R. China
• 2010 Natural Science’s First Prize of Hubei Province (rank #4)
• 2005 National (Top 100) Excellent Doctoral Dissertation of P.R. China
• 2004 Provincial Excellent Doctoral Dissertation of Hubei of P. R. China
• 2002 National Academia Sinica Award of China
• Thermal Physics