PUBLICATIONS
Papers and book chapters, etc. |
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Peer reviewed articles:
Google Scholar Citations: https://scholar.google.com/citations?user=aQg2lRoAAAAJ&hl=en
2020
- Yan Y, Tao H, He J, Huang S-Y.* The HDOCK server for integrated protein-protein docking. Nature Protocols, 2020; doi: 10.1038/s41596-020-0312-x. link
Wen Z, He J, Huang S-Y.* Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinformatics, 2020;36(2):478-486. link - He J, Tao H, Yan Y, Huang S-Y.*, Xiao Y.* Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2. Viruses, 2020; 12: 428. link
- 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, 2020; doi: 10.1021/acs.jcim.0c00058. link
- 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, 2020; doi: 10.1002/prot.25874. link
2019
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, DOI: 10.1093/nar/gkz412, 2019 (in press). [Online] [Server] He J, Tao H, Huang S-Y.* Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinformatics, DOI: 10.1093/bioinformatics/btz388, 2019 (in press). link 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 Zhang Y, Huang S-Y.* Exploring the Binding Mechanism and Dynamics of EndoMS/NucS
to Mismatched dsDNA. Int J Mol Sci, 2019;20(20). pii: E5142. doi:
10.3390/ijms20205142. link Zhang Y, Tao H, Huang S-Y.* Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1. Int J Mol Sci, 2019 Jul 6;20(13). pii: E3325. link 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, DOI: 10.1021/acs.jcim.9b00057, 2019 (in press). link Yan Y, Huang S-Y.* A non-redundant benchmark for symmetric protein docking. Big Data Mining and Analytics, 2: 92-99, 2019. link Yan Y, Huang S-Y.* CHDOCK: a hierarchical docking approach for modeling Cn symmetric homo-oligomeric complexes. Biophysics Reports, 5: 65-72, 2019. link 2018
Yan Y, Huang S-Y.* Protein-Protein Docking with Improved Shape Complementarity. International Conference on Intelligent Computing, 600-605, 2018. link 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 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 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 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 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 Wang X, Huang S-Y.* Optimizing the atom types of proteins through iterative knowledge-based potentials. Chinese Physics B, 27: 20503-020503, 2018. link Yan Y, Huang S-Y.* RRDB: A comprehensive and nonredundant benchmark for RNA-RNA docking and scoring. Bioinformatics, 34: 453-458, 2018. link 2017
Yan Y, Zhang D, Huang S-Y.* Efficient conformational ensemble generation of
protein-bound peptides. Journal of Cheminformatics, 9: 59, 2017. link 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 Huang S-Y.* Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Briefings in Bioinformatics, 19: 982-994, 2017. link 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 2016
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 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 2015
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 2014
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 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 Huang, S.-Y.* Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discovery Today, 19: 1081-1096, 2014. link 2013
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 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 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 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 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 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 2011
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 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 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 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 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 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 2010
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 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 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 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 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 Huang, S.-Y., Zou, X. Advances and challenges in protein-ligand docking. International Journal of Molecular Science, 11: 3016-3034, 2010. link 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 2009
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 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 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 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 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 2008
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 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 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 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 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 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 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 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 2007
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 Huang, S.-Y., Zou, X. Efficient molecular docking of NMR structures: Application to HIV-1 protease. Protein Science, 16: 43-51, 2007. link 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 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 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 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 2006
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 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 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 2004
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 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 2003
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 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 2002
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 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 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 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 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 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 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 Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Multiparticle random walks on a deformable medium. Physical Review E, 66: 041112, 2002. link Huang, S.-Y., Zou, X.-W., Jin, Z.-Z. Directed random walks in continuous space. Physical Review E, 65: 052105, 2002. link 2001
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 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 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 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 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 2000
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 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 1999
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:
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 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). 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).
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