Huang Research Group at HKUST

Book Chapters

• Jiang, H., Zhu, L., Héliou, A., Gao, X.*, Bernauer, J.*, and Huang, X*. "Elucidating Mechanisms of Molecular Recognition between human Argonaute and miRNA using Computational Approaches", Book Chapter, Methods in Molecular Biology, Drug Target miRNA, (Editor M.F. Schmidt), Springer, vol. 1517, (2017), DOI: 10.1007/978-1-4939-6563-2_18
• Zhang, L., Jiang, H., Sheong, F.K., Pardo-Avila, F., Cheung, P.P., and Huang, X. "Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and their Recognition with Ligands", Book Chapter, Methods in Enzymology, Computational approaches for studying Enzyme Mechanism, (Editor G.A. Voth), Elsevier, 578, 343–371, (2016)
• Huang, X, Zhou, R. H. and Berne, B.J. "Introduction to Molecular Dynamics and Enhanced Sampling Algorithms", Book Chapter, MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor R. Zhou), Taylor & Francis, Oxford, United Kingdom, (2014)
• Da, L., Sheong, F.K., Silva, D., Huang, X. "Application of Markov State Models to Simulate Long Timescale Dynamics of Biological Macromolecules", Book Chapter, Protein Conformational Dynamics, Advances in Experimental Medicine and Biology. 805, 29-66, Springer, (2014)
• Huang, X., Fabritiis, G.D., "Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations", Book Chapter, An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, 107-114, Springer, (2014)

Full List of Publications

2021

• Wang, Y., Chong, T.H., Unarta, I.C., Xu, X., Suarez, G.D., Wang, J., Lis, J.T., Huang, X., Cheung, P.*, "EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error ", Bio-protocol, 11(4), (2021)
• Zhang, L.*, Zhang, D., Yuan, C., Wang, X., Li, Y., Jia, X., Gao, X., Yen, H.-L.*, Cheung, P.*, Huang, X.*, "Role of 1'-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication", Phys. Chem. Chem. Phys., Accpeted, (2021), bioRxiv
• Wang, X., Unarta, I.C., Cheung P.P.H., Huang, X.* "Elucidating Molecular Mechanisms of Functional Conformational Changes of Proteins via Markov State Models", Curr. Opin. Struct. Biol, 67, 69-77, (2021)

2020

• Cao, Z., Wang, X., Huang, X., Mak, H.Y. "Are endoplasmic reticulum subdomains shaped by asymmetric distribution of phospholipids? Evidence from a C. elegans model system", BioEssays, (2020), DOI: 10.1002/bies.202000199
• Peng, S., Wang, X., Zhang L.*, He, S., Zhao, X.S, Huang, X.*, Chen, C.* "Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov State Models", Proc. Nat. Acad. Sci. U.S.A., 117 (36), 21889-21895, (2020)
• Cao, S., Montoya-Castillo, Andres., Wang, W., Markland, T.*, Huang, X.*, "On the Advantages of Exploiting Memory in Markov State Models for Biomolecular Dynamics", J. Chem. Phys.,153, 014105, (2020)
• He, Y., Lei, J., Pan, X., Huang, X.*, Zhao, Y.*, "The hydrolytic water molecule of Class A Beta-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis", Scientific Report, 10, 10205, (2020)
• Chan, K.H., Tse, L.H., Huang, X., Wong, Y.H., "Molecular basis defining the selectivity of substituted isoquinolinones for the melatonin MT2 receptor", Biochemical Pharmacology, Published On-line (2020), DOI: 10.1016/j.bcp.2020.114020
• Cheung, P., Jiang, B., Booth, G.T., Chong, T.H., Unartar, I.C., Wang, Y., Suarez, G.D., Wang, J.*, Lis, J.T.*, Huang, X.*, "Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-On Circular-Sequencing Coupled with Background Error Modeling", J. Mol. Biol., 432(13), 3933-3949(2020)
• Choy, K., Wong, A., Kaewpreedee, P., Sia, S., Chen, D., Hui, K., Chu, D., Chan, M., Cheung, P., Huang, X., Peiris, M., Yen, H-L, "Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro", Antiviral Research, 178: 104786, (2020)
• Pan, C., Liu, C., Peng, J., Ren, P.*, Huang, X.*, "Three-site and Five-site Fixed-charge Water Models Compatible with AMOEBA Force Field", J. Comput. Chem., 41:1034–1044, (2020)

2019

• Lam, J.H., Li, Y., Zhu, L., Umarov, R., Jiang, H., Heliou, A., Sheong, F.K., Liu, T., Long, Y., Li, Y., Fang, L., Altman, R., Chen, W., Huang, X.*, Gao, X.*, "A deep learning framework to predict binding preference of RNA constituents on protein surface", Nature Communications, 10, 4941, (2019)
• Tu, Y., Yu, Y., Zhou, Z., Xie, S., Yao, B., Guan, S., Situ, B., Liu, Y., Kwok, R.T.K., Lam, J.W.K., Chen, S., Huang, X.,Zeng, Z., Tang, B.Z., Specific and quantitative detection of albumin in biological fluids by tetrazolate-functionalized water-soluble AIEgens, ACS Appl. Mater. Interfaces, (2019), DOI: 10.1021/acsami.9b10359
• Zhao, Z., Zheng, X., ..., Lam, J. , Huang, X., Phillips, D., Wang, H., Tang, B.Z., Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process, Nature Communications, 10 (1), 2952, (2019)
• Konovalov, K.A., Pardo-Avila, F., Tse, C.K.M., Oh, J., Wang, D.*, Huang, X.*, “8-oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II”, J. Biol. Chem., (2019), DOI: 10.1074/jbc.RA118.007333
• Cao, S., Konovalov, K., Unarta, I.C., Huang, X.*, "Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute-Solvent Interface", Advanced Theory and Simulations, 1900049, (2019)
• Zhu, L., Liang, T., Sheong, F.K., Cao, S., Unarta, I.C., Liu, S., Huang, X.*,“TAPS: A Travelling-salesman Based Automated Path Searching Method for Functional Conformational Changes of Biological Macromolecules”, J. Chem. Phys., Accepted, (2019)
• Wang, L., Chen, J., Zeng, X., Cheung, P.P.H., Zheng, X., Shi, X., Ren, L.*, Huang, X.*, Wang, Y.*"Mechanistic Insights and Rational Design of the Versatile Surface with Cells/Bacteria Recognition Capability via Orientated Fusion Peptides", Adv. Sci., Accepted, (2019), DOI: 10.1002/advs.201801827
• Konovalov, K.A., Pardo-Avila, F., Tse, C.K.M., Oh, J., Wang, D.*, Huang, X.*, “8-oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II”, J. Biol. Chem., (2019), DOI: 10.1074/jbc.RA118.007333
• Hsieh, S.T., Zhang, L., Ye, D.W., Huang, X.*, Cheng, Y.C.* "A Theoretical Study on the Dynamics of Light Harvesting in the Dimeric Photosystem II Core Complex: Regulation and Robustness of Energy Transfer Pathways", Faraday Discuss., (2019), DOI: 10.1039/C8FD00205C
• Tse,C.K.M., Xu, J., Xu, L., Sheong, F.K., Wang, S., Chow, H.Y., Gao, X., Li, X., Cheung, P.P.H.*, Wang, D.*, Zhang, Y.*, Huang, X.*, "Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate ", Nature Catalysis, Published On-line, (2019), DOI:10.1038/s41929-019-0227-5
• Lei, J., Sheng, G., Cheung, P.P.H., Wang, S., Li, Y., Gao, X., Zhang, Y.*, Wang, Y.*, Huang, X.*, "Two Symmetric Arginine Residues Play Distinct Roles in Thermus thermophilus Argonaute DNA Guide Strand-mediated DNA Target Cleavage", Proc. Nat. Acad. Sci. U.S.A., 116 (3) 845-853, (2019)

2018

• Xian, Y., Gu, H., Wang, W., Huang, X., Yao, Y., Wang, Y., Cai, J.F., "Data-Driven Tight Frame for Cryo-EM Image Denoising and Conformational Classification", IEEE GlobalSIP, 544-548, (2018)
• Konovalov, K.A., Wang, W.,Huang, X.*, “Conformational selection turns on phenylalanine hydroxylase”, J. Biol. Chem.,293, 19544-19545, (2018)
• Zhou, Y., Li, C., Peng, J., Xie, L., Meng, L., Li, Q., Zhang, J., Li, D.X, Li, X.*, Huang, X.*, Li, X*,“DNA-encoded Dynamic Chemical Library and Its Applications in Ligand Discovery”, J. Am. Chem. Soc., 140(46), 15859–15867, (2018)
• Wang, W., Liang, T., Sheong, F.K., Fan, X.*, Huang, X.*,“An Efficient Bayesian Kinetic Lumping Algorithm to Identify Metastable Conformational States via Gibbs Sampling ”, J. Chem. Phys.,149, 072337, (2018)
• Peng, J., Wang, W., Yu, Y., Gu, H., Huang, X.*,“Clustering algorithms to Analyze Molecular Dynamics Simulation Trajectories for Complex Chemical and Biological Systems”, Chin. J. Chem. Phys., Accepted, (2018) (Invited article dedicated to the 60th Anniversary of our Alma Mater: USTC, and all the authors obtained B.S. degrees from USTC)
• Gu, S., Fu, W.Y.,Fu, AKY, Tong, EPS, Ip, FCF.,Huang, X., Ip, N.Y., “Identification of new EphA4 inhibitors by virtual screening of FDA-approved drugs ”, Scientific Reports, 8 (1), 7377 (2018)
• Zeng, X., Li, Z.*, Zheng, X., Zhu, L., Sun, Z., Lu, Z., Huang, X.*,“Improving the Productivity of Monodisperse Polyhedral Cages by Rational Design of Kinetic Self-assembly Pathways”, Phys. Chem. Chem. Phys., (2018), DOI:10.1039/C8CP00522B
• Zeng, X., Zhu, L., Zheng, X., Cecchini, M.*, Huang, X.*,“Harnessing Complexity in Molecular Self-Assembly by Computer Simulations”, Phys. Chem. Chem. Phys., 20, 6767-6776 (2018)
• Molodtsov, V., Sineva, E., Zhang, L., Huang, X., Cashel, M., Ades, S.E., Murakami, K.S. "Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA", Molecular Cell, Volume 69, Issue 5, Pages 828-839, (2018)
• Unarta, I.C., Zhu, L., Tse, K.M., Cheung, P.P.H., Yu, J., Huang, X.*,“Molecular Mechanisms of RNA Polymerase II Transcription Elongation Elucidated by Kinetic Network Models”, Curr. Opin. Struct. Biol,49, 54-62, (2018)
• Bratkowski, M., Unarta, I.C., Zhu, L., Shubbar, M., Huang, X., Liu, X., “Structural Dissection of an Interaction between Transcription Initiation and Termination Factors Implicated in Promoter−Terminator Crosstalk”, J. Biol. Chem.,293, 1651-1665, (2018)

2017

• Zhu, J., Zhou, Q., Shang, Y., Li, H., Peng,M., Ke, X., Weng,Z., Zhang,R., Huang, X., Li. S.C., Feng, G., Lu, Y., Zhang, M., “Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs”, Cell Reports, 1-11, (2017), doi: 10.1080/00268976.2017.1416195
• Cao, S., Zhu, L., Huang, .X.*, “3DRISM-HI-D2MSA: An improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute-solvent electrostatic interactions”, Mol. Phys., 1-11, (2017), doi: 10.1080/00268976.2017.1416195
• Feng, H.T., Zheng, X., Gu, X., Chen, M., Lam, J., Huang, X., Tang, B.Z.,"White-Light Emission of a Binary Light-Harvesting Platform Based on an Amphiphilic Organic Cage", Chem. Mater., (2017), DOI: 10.1021/acs.chemmater.7b04703
• Jiang, M., Gu, X., Kwok, R., Li, Y., Sung, H., Zheng, X., Zhang, Y., Lam, J., Williams, I.D., Huang, X., Wong, Tang, B.Z. "Multifunctional AIEgens: Ready Synthesis, Tunable Emission, Mechanochromism, Mitochondrial, and Bacterial Imaging Authors", Adv. Funct. Mater., 1704589, (2017)
• Zhang, H., Zheng, X., ... Huang, X., Wong, K.S., Kwok, R., Sung, H., Williams, I.D., Qin, A., Lam, J.W.Y., Tang, B.Z., "Why do simple molecules with “isolated” phenyl rings emit visible light?", J. Am. Chem. Soc., 139 (45), 16264–16272, (2017)
• Tian, Y., Zeng, X., Li, J., Jiang, Y., Zhao, H., Wang, Y., Huang, .X.*, Li, Z.*, “Achieving Enhanced Cell Penetration of Short Conformationally Constrained Peptides through Amphiphilicity Tuning”, Chemical Science, 8, 7576-7581 (2017)
• Wang, W., Cao, S., Zhu, L., Huang, X.*, “Constructing Markov State Models to Elucidate the Functional Conformational Changes of Complex Biomolecules”, WIREs Comput Mol Sci., e1343, (2017), DOI:10.1002/wcms.1343
• Chevalier, A, Silva, D.A., Rocklin, G.J., Hicks, Vergara, Murapa, Bernard, Zhang, L.,..., Huang, X., Jin, R., Wilson, I.A., Fuller, D.H., Baker, D., “Massively parallel de novo protein design for targeted therapeutics”, Nature, 550, 74-79, (2017)
• Peng, H., Zheng, X., Han, T., Kwok, R.T.K., Lam, J.W.Y., Huang, X., Tang, B.Z., "Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers", J. Am. Chem. Soc., 139 (29), 10150, (2017)
• Meng, L., Sheong, F.K., Zeng, X., Zhu, L., Huang, X.*, “Path Lumping: An Efficient Algorithm to Identify Metastable Path Channels for Conformational Dynamics of Multi-body Systems ”, J. Chem. Phys., 147, 044112, (2017)
• Zhai, Y., Li, N., Jiang, H., Huang, X., Gao, N., Tye, B. (2017) "Unique roles played by each of the non-identical MCM subunits in DNA Replication Licensing", Molecular Cell, 67 (2), 168-179, (2017)
• Jiang, L., Cao, S., Cheung, P.P., Zheng, X., Leung, C.W.T., Peng, Q., Shuai, Z., Tang, B.Z., Yao, S.*, Huang, X.*, “Real-Time Monitoring of Hydrophobic Aggregation Reveals a Critical Role of Cooperativity in Hydrophobic Effect”, Nature Communications, 8, 15639, (2017)
• Zheng, X., Zhu, L., Zeng, X., Meng, L., Zhang, L., Wang, D., Huang, X.*, “Kinetics-Controlled Amphiphiles Self-Assembly Processes”, J. Phys. Chem. Lett., 8, 1798–1803, (2017)
• Zhang, Q., Zheng, X., Kuang, G., Wang, W., Zhu, L., Pang, R., Shi, X., Shang, X., Huang, X., Liu, P., Lin, N., “Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces”, J. Phys. Chem. Lett., 8, 1241-1247, (2017)
• Chen, C., Song, Z., Zheng, X., He, Z., Liu, B., Huang, X., Kong, D., Ding, D., Tang, B.Z.“AIEgen-based Theranostic System: Targeted Imaging of Cancer Cells and Adjuvant Amplification of Antitumor Efficacy of Paclitaxel” , Chemical Science, 8, 2191-2198, (2017)
• Li, J., Chen, Y., Deng, Y., Unarta, I.C., Lu, Q., Huang, X., Zhang, M., “Ca2+-induced Rigidity Change of the Myosin VIIa IQ Motif-Single α-Helix Lever Arm Extension”, Structure, 25:1-13, (2017)
• Wen, J., Gu, S., Gao, X., Huang, X., and Wang, W., “Maltose Binding Protein Effectively Stabilizes the Partially Closed Conformation of the ATP-binding Cassette Transporter MalFGK2”, Phys. Chem. Chem. Phys., Accepted, (2017), DOI: 10.1039/C6CP07943A
• Liu, S., Zhu, L., Sheong, F.K., Wang, W., Huang, X., “Adaptive Partitioning by Local Density-peaks (APLoD): An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories”,J. Comput. Chem. , 38(3):152-160, (2017)
• Pan, X., He, Y., Lei, J., Huang, X., and Zhao, Y.,“Crystallographic snapshots of Class A β-lactamase catalysis reveal structural changes that facilitate β-lactam hydrolysis”,J. Bio. Chem. , 292 (10), 4022-4033, (2017)
• Zhu, L., Jiang, H., Sheong, F.K., Cui, X.,Wang, Y., Gao, X.*, Huang, X.*, “Understanding the Core of RNA Interference: the Dynamic Aspects of Argonaute-mediated Processes”, Prog. Biophys. Mol. Bio. , 128, 39-46, (2017)

2016

• Feng, Y., Zhang, L., Wu, S., Gao, X., Liu, J.*, Huang, X.*, Wang, W.*, “Multiple Metastable Conformations Co-exist in the Apo-Glutamine Binding Protein Structural Ensemble Revealed by Tightly Coupled Experimental and Computational Approaches”, Angew. Chem. Int. Ed., 55 (45), 13990–13994, (2016)
• Qiao, Q.*, Qi, R., Wei, G.*, Huang, X.*, “Dynamics of the Conformational Transitions during the Dimerization of an Intrinsically Disordered Peptide: a Case Study on the Human Islet Amyloid Polypeptide Fragment ”, Phys. Chem. Chem. Phys.,18, 29892-29904, (2016)
• Lin, H., Chen, S., Hu, H., Zhang, L., Ma, T., Lai, J. Y. L., Li, Z., Qin, A., Huang, X., Tang, B. and Yan, H. , "Reduced Intramolecular Twisting Improves the Performance of 3D Molecular Acceptors in Non-Fullerene Organic Solar Cells”, Adv. Mater., , Published On-line, (2016) DOI:10.1002/adma.201600997
• Zheng, J., Wang, L., Zeng, X., Zheng, X., Zhang, Y., Liu, S., Shi, X., Wang, Y., Huang, X., Ren, L., “Controlling the Integration of Polyvinyl-pyrrolidone onto Substrate by Quartz Crystal Microbalance with Dissipation To Achieve Excellent Protein Resistance and Detoxification”, ACS Appl. Mater. Interfaces, 8(29), 18684-18692, (2016)
• Zheng, X., Peng, Q., Zhu, L., Xie, Y., Huang, X., Shuai, Z., “Unraveling the aggregation effect on amorphous phase AIE luminogens: A computational study”, Nanoscale, 8, 15173-15180, (2016)

• Zhu, L., Sheong, F. K., Zeng, X., Huang, X., “Elucidating conformational dynamics of multi-body systems by constructing Markov State Models”, Phys. Chem. Chem. Phys., Published On-line, (2016), DOI: 10.1039/C6CP02545E
• Zeng, X., Li, B., Qiao, Q., Zhu, L., Lu, Z.-Y., Huang, X., “Elucidating Dominant Pathways of the Nano-particle Self-Assembly Process”, Phys. Chem. Chem. Phys., 18, 23494-23499, (2016)

• Qiao, Q., Zhang, H., Huang, X., “Enhancing Pairwise State-transition Weights (EPSW): A New Weighting Scheme in Simulated Tempering that can Minimize Transition Time between a Pair of Conformational States”, J. Chem. Phys., 144, 154107, (2016)
• Hwang, C., Xu, L., Wang, W., Ulrich, S., Zhang, L., Chong, J., Shin, J. H., Huang, X., Kool, E., McKenna, C., Wang, D. “Functional Interplay between NTP Leaving Group and Base Pair Recognition during RNA Polymerase II Nucleotide Incorporation Revealed by Methylene Substitution”, Nucl. Acids Res., 44(8):3820-8, (2016)
• Zhang, L., Pardo, F., Unarta, I.C., Cheung, P., Wang, G., Wang, D., and Huang, X. “Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models”, Accounts of Chemical Research, 49 (4), 687–694, (2016)
• Da, L., Pardo, F., Xu, L., Silva, D., Zhang, L., Gao, X., Wang, D., Huang, X.“Bridge Helix Bending Promotes RNA Polymerase II Backtracking Through a Critical and Conserved Threonine Residue”, Nature Communications, 7, 11244, (2016)
• Zhu, L., Jiang, H., Sheong, F.K., Cui, X., Gao, X., Wang, Y., Huang, X. "A Flexible Domain-domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus Thermophilus", J. Phys. Chem. B, 120(10), 2709–2720, (2016)
• Tian, Y., Li, J., Zhou, H., Zeng, X., Wang, D., Liu, Q., Niu, X., Huang, X., Xu, N., Li, Z. “Stapling of unprotected helical peptides via photo-induced intramolecular thiolyne hydrothiolation”, Chem. Sci., Published On-line, (2016), DOI: 10.1039/C6SC00106H
• Li, H., Zheng, X., Su, H., Lam, J.W.Y., Wong, K.S., Xue, S., Huang, X., Huang, X., Li, B., Tang, B.Z., "Synthesis, optical properties, and helical self-assembly of a bivalinecontaining tetraphenylethene.", Scientific Reports, 6, 19277-19285,(2016)

2015

• Wang, E., He, Z., Zhao, E., Meng, L., Schütt, C., Lam, J.W.Y., Sung, H.Y., Williams, I.D., Huang, X., Herges, R., Tang, B.Z., "Aggregation-Induced-Emission-Active Macrocycle Exhibiting Analogous Triply and Singly Twisted Möbius Topologies", Chemistry-A European Journal, 21(33), 11707-11711, (2015)
• Cao, S., Sheong, F.K., Huang, X., “Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity: An Analytical Theory to Compute Solvation Properties of Large Hydrophobic Solutes in the Mixture of Polyatomic Solvent Molecules”, J. Chem. Phys., 143, 054110, (2015)
• Jiang, H., Sheong, F.K., Zhu, L., Gao, X., Bernauer, J., Huang, X., "Markov State Models Reveal a Two-step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding Followed by Structural Re-arrangement", PLoS. Comp. Bio., 11(7): e1004404, (2015)
• Zhang, L., Silva, D.A., Pardo-Avila, F., Wang, D., Huang, X., "Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes", PLoS. Comp. Bio., 11(7), e100435, (2015)
• Xu, L., Wang, W., Zhang, L., Chong, J., Huang, X., Wang, D., "Impact of template backbone heterogeneity on RNA polymerase II transcription", Nucl. Acids Res., 43 (4), 2232-2241, (2015)
• Sheong, F.K., Silva, D.A., Meng, L., Zhao, Y., Huang, X. "Automatic state Partitioning for Multi-body systems (APM): An Efficient Algorithm for Constructing Markov State Models to Elucidate Conformational Dynamics of Multi-body Systems", J. Chem. Theory Comput., 11 (1), 17–27, (2015)
• Liu, Y., Mu, C., Jiang, K., Zhao, J., Li, Y., Zhang, L., Li, Z., Lai, J., Hu, H., Ma, T., Hu, R., Yu, D., Huang, X., Tang, B., Yan, H. "A Tetraphenylethylene Core-Based 3D Structure Small Molecular Acceptor Enabling Efficient Non-Fullerene Organic Solar Cells", Adv. Mater., 27(6), 1015-1020, (2015)
• Yu, J., Da, L.T., Huang, X., "Constructing Kinetic Models to Elucidate Structural Dynamics of a Complete RNA Polymerase II Elongation Cycle", Phys. Bio., 12, 016004, (2015)
• Lu, L., Meehan, M., Gu, S., Chen, Z., Zhang, W., Zhang, G., Liu, L., Huang, X., Dorrestein, P., Xu, Y., Moore, B., Qian, P.,"Mechanism of Action of Thalassospiramides, A New Class of Calpain Inhibitors", Sci. Rep., 5, 8783, (2015)
• Zhao, E., Lam, J., Meng, L., Hong, Y., Deng, H., Bai, G., Huang, X., Hao, J., Tang, B., "Aoly[(maleic anhydride)-alt-(vinyl acetate)]: A Pure Oxygenic Nonconjugated Macromolecule with Strong Light Emission and Solvatochromic Effect", Macromolecules, 48 (1), 64–71, (2015)
• Erjing Wang, Zikai He, Engui Zhao, Luming Meng, Christian Schütt, Jacky WY Lam, Herman HY Sung, Ian D Williams, Xuhui Huang, Rainer Herges, Ben Zhong Tang. "Aggregation-Induced-Emission-Active Macrocycle Exhibiting Analogous Triply and Singly Twisted Möbius Topologies", Chemistry-A European Journal, 21(33), 11707-11711, (2015)
• Jingbo Zhao , Yunke Li , Jianquan Zhang , Lu Zhang , Joshua Yuk Lin Lai , Kui Jiang , Cheng Mu , Zhengke Li , Chun Lam Clement Chan , Adrian Hunt , Subhrangsu Mukherjee , Harald Ade , Xuhui Huang and He Yan. "The influence of spacer units on molecular properties and solar cell performance of non-fullerene acceptors.", J. Mater. Chem. A, 21 (33), 11707-11711, (2015)

2014

• Gu, S., Silva, D.A., Meng, L., Yue, A., Huang, X., "Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein using Markov State Model Analysis", PLoS. Comp. Bio., 10(8):e1003767, (2014)
• Xu, L, Zhang, L., Chong, J., Xu, J., Huang, X., Wang, D., "A Chemical Perspective on Transcriptional Fidelity and Evolution: Asymmetric Recognition of Phosphodiester Linkage by RNA Polymerase II", Proc. Nat. Acad. Sci. U.S.A., 111, E3269–E3276, (2014)
• Fu, A., Hung, K.W., Huang, H., Gu, S., Shen, Y., Cheng, Ip, F.,, Huang, X, Fu, W.,,Ip, N.Y., "Blockade of EphA4 signaling ameliorates hippocampal synaptic dysfunctions in mouse models of Alzheimer's disease", Proc. Nat. Acad. Sci. U.S.A., 111, 9959-9964, (2014)
• Silva, D., Weiss. D., Pardo-Avila, F., Da, L., Levitt, M., Wang, D., Huang, X., "Millisecond Dynamics of RNA Polymerase II Translocation at Atomic Resolution", Proc. Nat. Acad. Sci. U.S.A., 111, 7665-7670, (2014)

Recommended on Faculty of 1000 Prime

• Zhang, L., Silva, D.A., Yue, A., Zhang, H., Yan, Y., Huang, X., "Dynamic Protein Conformations Preferentially Drive Energy Transfer along Active Chain of the Photosystem-II Reaction Center", Nature Communications, 5:4170 doi: 10.1038/ncomms5170, (2014)

2013

• Qiao, Q., Bowman, G.R., Huang, X., “Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation”, J. Am. Chem. Soc., 135 (43), 16092–16101, (2013)

• Pardo-Avila, F., Da, L., Wang, Y., Huang, X., “Theoretical Investigations on Elucidating Fundamental Mechanisms of Catalysis and Dynamics Involved in Transcription by RNA Polymerase”, J. Theor. Comput. Chem., 12(8), 1341005, (2013) (Invited Review)
• Bowman, G.R., Meng, L., Huang, X., “Quantitative comparison of alternative methods for coarse-graining biological networks ”, J. Chem. Phys., 139, 121905, (2013)
• Yao, Y., Cui, R.Z., Bowman, G.R., Silva, D.A., Sun, J., Huang, X., “Hierarchical Nystrom Methods for Constructing Markov State Models for Conformational Dynamics ”, J. Chem. Phys., 138, 174106, (2013)
• Da, L., Pardo-Avila, F., Wang, D., Huang, X., “A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase”, PLoS. Comp. Bio., 9(4): e1003020, (2013)

Recommended on Faculty of 1000 Prime

• Zhao, Y., Sheong, F.K., Sun, J., Sander, P., Huang, X.“A Fast Parallel Clustering Algorithm for Molecular Simulation Trajectories”, J. Comput. Chem., 34(2), 95-104, (2013)

2012

• Song, J., Gao, F., Cui, R.Z., Shuang, F., Liang, W., Huang, X., Zhuang, W., "Investigating the Structural Origin of Trpzip2 Temperature Dependent Unfolding Fluorescence Lineshape Based on a Markov State Model Simulation", J. Phys. Chem. B., 116(42), 12669-12676, (2012)
• Zhang, L., Silva, D.A., Yan, Y.J., Huang, X.“Force Field Development for Cofactors in the Photosystem II ”, J. Comput. Chem., 33 (25), 1969–1980, (2012)
• Liu, J., Su, H., Meng, L., Zhao, Y., Ng, C.Y., Lu, P., Faisal, M., Lam, W.Y., Huang, X., Wu, H., Wong, K.S., Tang, B., "What makes efficient circularly polarised luminescence in the condensed phase: Aggregation-induced circular dichroism and light emission", Chem. Sci., 3, 2737-2747, (2012)
• Da, L., Wang, D., Huang, X., “Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II”, J. Am. Chem. Soc., 134 (4), 2399, (2012)

Recommended on Faculty of 1000 Prime

• Hong, Y., Meng, L., Chen, S., Leung, C., Da, L., Faisal, M., Silva, D.A., Liu, J., Lam, J., Huang, X., Tang, B., “Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics”, J. Am. Chem. Soc., 134 (3), 168, (2012)
• Flores, S., Bernauer, J., Shin, S., Zhou, R., Huang, X., “Multi-scale modeling of macromolecular biosystems”, Briefings in Bioinformatics, 13(4), 395-405, (2012)
• Cui, R.Z., Silva, D.A., Song, J., Bowman, G.R., Zhuang, W., Huang, X., “Bridging the gap between optical spectroscopic experiments and computer simulations for fast protein folding dynamics”, Curr. Phys. Chem., 2, 45-58, (2012)

2011

• Liu, X., Bushnell D.A., Silva, D.A., Huang, X., and Kornberg R.D. “Initiation Complex Structure and Promoter Proofreading”, Science, 333, 633-637, (2011)
• Silva, D.A., Bowman, G.R., Sosa-Peinado, A., Huang, X., "A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein", PLoS. Comp. Bio., 7(5), e1002054, (2011)
• Zhuang, W., Cui, R.Z., Silva, D.A., Huang, X., “Simulating the T-jump triggered unfolding dynamics of Trpzip2 peptide and its time resolved IR and 2DIR signals using Markov State Model Approach”, J. Phys. Chem. B., 115, 5415-5424, (2011)
• Bernauer, J., Huang, X., Sim, A.Y.L., Levitt, M.“Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation”, RNA, 17, 1066-1075, (2011)
• Bernauer, J., Flores, S., Huang, X., Shin, S., Zhou, R., “Multi-scale modeling of biosystems: From molecular to mesoscale”, Proceedings of the Pacific Symposium on Biocomputing, 177-180, (2011)

2010

• Huang, X.*, Wang, D, Weiss, D.H., Bushnell, D.A., Kornberg, R.D, and Levitt, M.*,"RNA Polymerase II Trigger Loop Residues Stabilize and Position the Incoming Nucleotide Triphosphate in Transcription" Proc. Nat. Acad. Sci. U.S.A., 107, 15745-15750, (2010)

Recommended on Faculty of 1000 Prime

• Wang, D., Zhu, G., Huang, X., Lippard, S.J., “X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct”,Proc. Nat. Acad. Sci. U.S.A., 107, 9584-9589, (2010).

Recommended on Faculty of 1000 Prime

• Bowman, G.R., Huang, X., Pande V.S.,"Network models for molecular kinetics and their initial applications to human health”, Cell Research, 20, 622–630, (2010)
• Young T., Hua L., Huang, X., Abel R., Friesner R., Berne B.J., “Dewetting Transitions in Protein Cavities”, Proteins, 78, 1856-1869, (2010)
• Huang, X.*, Yao Y., Sun J., Bowman G.R.,Guibas L., and Carlsson G.. and Pande V.S. “Constructing Multi-resolution Markov State Models(MSMs) to elucidate RNA hairping folding mechanisms”, Proceedings of the Pacific Symposium on Biocomputing, 15, 228-239, (2010)

2003-2009

• Huang, X., Bowman, G. R., Bacallado, S., and Pande, V. S. “Rapid Equilibrium Sampling Initiated from Non-equilibrium Data”, Proc. Nat. Acad. Sci. U.S.A., 106, 19765-19769, (2009)
• Bowman, G. R., Huang, X. and Pande, V. S. “Using generalized ensemble simulations and Markov state models to identify conformational states”, Methods, 49, 197-201, (2009)
• Wang D, Bushnell D.A., Huang, X, Westover K.D., Levitt M, and Kornberg R.D. “Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution” , Science, 324, 1203-1206, (2009)
• Kelley, N., Huang, X, Tam, S., Spiess C., Frydman, J., Pande, V. S. “The Predicted Structure of the Headpiece of the Huntingtin Protein and its Implications on Huntingtin Aggregation.” J. Mol. Bio., 338, 919-927, (2009)
• Yao Y, Sun J, Huang, X, Bowman G.R., Lesnik M, Singh G, Pande V.S., Guibas L, and Carlsson G. “Topological Methods for Exploratory Pathway Analysis of Complex Biomolecular Systems”, J. Chem. Phys., 130, 144115, (2009)
• Bowman G.R., Huang, X, Yao Y, Sun J, Carlsson G, Guibas L., Pande V.S. “Structural Insight into RNA Hairpin Folding Intermediates.” J. Am. Chem. Soc., 130, 9676–9678, (2008)
• Huang, X., Bowman, G. R., and Pande, V. S. “Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.” J. Chem. Phys. 128, 205106, (2008)
• Hu, Z., Huang, X., Annapureddy H.V.R.,and Margulis C.J. “Molecular Dynamics Study of the Temperature-Dependent Optical Kerr Effect Spectra and Intermolecular Dynamics of Room Temperature Ionic Liquid 1-Methoxyethylpyridinium Dicyanoamide”, J. Phys. Chem. B, 112 (26), 7837–7849, (2008)
• Huang, X., Hagen, M., Kim, B., Friesner, R.A., Zhou, R and Berne, B.J. “Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems” J. Phys. Chem. B. 111, 5405-5410, (2007)
• Hua, L., Huang, X., Liu, P., Zhou, R. and Berne, B.J. “Nanoscale Dewetting Transition in Protein Complex Folding.” J. Phys. Chem. B. 111, 9069-9077, (2007)
• Liu, P., Huang, X., Zhou, R., Berne, B.J. “Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent.” J. Phys. Chem. B 110, 19018-19022, (2006)
• Hua, L., Huang X., Zhou, R., and Berne, B.J., “Dynamics of water confined in the interdomain region of a multidomain protein”, J. Phys. Chem. B., 110, 8, 3704-3711 (2006).
• Huang, X., Margulis, C.J., Li, Y. and Berne, B.J.,“Why is the Partial Molar Volume of CO2 So Small When Dissolved in a Room Temperature Ionic Liquid? Structure and Dynamics of CO2 Dissolved in [Bmim+] [PF6-].”, J. Am. Chem. Soc., 127, 50, 17842-17851 (2005).
• Liu, P., Huang, X., Zhou, R., Berne, B.J., “Observation of a dewetting transition in the collapse of the melittin tetramer”, Nature, 437, 159-162 (2005).
• Huang, X., Zhou, R. and Berne, B.J., “Drying and Hydrophobic Collapse of Paraffin Plated”, J. Phys. Chem. B, 109, 3546-3552 (2005).
• Zhou, R., Huang, X., Margulis, C.J., and Berne, B.J., “Hydrophobic Collapse in Multi-domain Protein Folding”, Science, 305, 1605-1609 (2004).
• Huang, X., Margulis, C.J., Berne, B.J. “Comment on "Do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces?” - Reply ” J. Phys. Chem. B 108 (26): 9373-9374,(2004)
• Huang, X., Margulis C.J., and Berne, B.J., “Dewetting-induced collapse of hydrophobic particles”, Proc. Nat. Acad. Sci., 100, 21, 11953-11958 (2003).
• Huang, X., Margulis, C.J., and Berne, B.J., “Do Molecules as Small as Neopentane Induce a Hydrophobic Response Similar to That of Large Hydrophobic Surfaces?” J. Phys. Chem. B, 107, 42, 11742-11748 (2003).