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Xuhui Huang, Ph.D. - Publications

Affiliations: 
2006 Columbia University, New York, NY 
 2010-2021 Chemistry Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 
 2021- Chemistry University of Wisconsin, Madison, Madison, WI 
Area:
Theoretical chemistry, biophysics, computational biology, statistical mechanics, structural biology
Website:
https://www2.chem.wisc.edu/users/xhuang
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126 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Qiu Y, Wiewiora RP, Izaguirre JA, Xu H, Sherman W, Tang W, Huang X. Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design. Jacs Au. 4: 3857-3868. PMID 39483225 DOI: 10.1021/jacsau.4c00503  0.625
2024 Wang D, Qiu Y, Beyerle ER, Huang X, Tiwary P. An Information Bottleneck Approach for Markov Model Construction. Arxiv. PMID 38947932  0.583
2024 Wang D, Qiu Y, Beyerle ER, Huang X, Tiwary P. Information Bottleneck Approach for Markov Model Construction. Journal of Chemical Theory and Computation. PMID 38859575 DOI: 10.1021/acs.jctc.4c00449  0.582
2023 Dominic AJ, Sayer T, Cao S, Markland TE, Huang X, Montoya-Castillo A. Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America. 120: e2221048120. PMID 36920924 DOI: 10.1073/pnas.2221048120  0.633
2022 Zheng X, Chan MH, Chan AK, Cao S, Ng M, Sheong FK, Li C, Goonetilleke EC, Lam WWY, Lau TC, Huang X, Yam VW. Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes. Proceedings of the National Academy of Sciences of the United States of America. 119: e2116543119. PMID 35298336 DOI: 10.1073/pnas.2116543119  0.464
2022 Gu H, Wang W, Cao S, Unarta IC, Yao Y, Sheong FK, Huang X. RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics. Physical Chemistry Chemical Physics : Pccp. PMID 34985469 DOI: 10.1039/d1cp03622j  0.31
2021 Zhu L, Jiang H, Cao S, Unarta IC, Gao X, Huang X. Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Communications Biology. 4: 1345. PMID 34848812 DOI: 10.1038/s42003-021-02822-7  0.636
2021 Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PP, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Research. PMID 34379778 DOI: 10.1093/nar/gkab660  0.399
2021 Wang Y, Yuan C, Xu X, Chong TH, Zhang L, Cheung PP, Huang X. The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription. Biophysical Chemistry. 277: 106652. PMID 34237555 DOI: 10.1016/j.bpc.2021.106652  0.367
2021 Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D. Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nature Chemical Biology. PMID 34140682 DOI: 10.1038/s41589-021-00817-3  0.317
2021 Quinn TR, Steussy CN, Haines BE, Lei J, Wang W, Sheong FK, Stauffacher CV, Huang X, Norrby PO, Helquist P, Wiest O. Microsecond timescale MD simulations at the transition state of HMGR predict remote allosteric residues. Chemical Science. 12: 6413-6418. PMID 34084441 DOI: 10.1039/d1sc00102g  0.318
2021 Konovalov KA, Wang W, Wang G, Goonetilleke EC, Gao X, Wang D, Huang X. A Comprehensive mechanism for 5-carboxylcytosine induced transcriptional pausing revealed by Markov state models. The Journal of Biological Chemistry. 100735. PMID 33991521 DOI: 10.1016/j.jbc.2021.100735  0.331
2021 Wang Y, Chong TH, Unarta IC, Xu X, Suarez GD, Wang J, Lis JT, Huang X, Cheung PP. EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error. Bio-Protocol. 11: e3921. PMID 33732808 DOI: 10.21769/BioProtoc.3921  0.34
2021 Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, Adamopoulos IE, Adeli K, Adolph TE, Adornetto A, Aflaki E, ... ... Huang X, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 1-382. PMID 33634751 DOI: 10.1080/15548627.2020.1797280  0.616
2020 Cao S, Montoya-Castillo A, Wang W, Markland TE, Huang X. On the advantages of exploiting memory in Markov state models for biomolecular dynamics. The Journal of Chemical Physics. 153: 014105. PMID 32640825 DOI: 10.1063/5.0010787  0.687
2020 Cheung PP, Jiang B, Booth GT, Chong TH, Unarta IC, Wang Y, Suarez GD, Wang J, Lis JT, Huang X. Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling. Journal of Molecular Biology. PMID 32325070 DOI: 10.1016/J.Jmb.2020.04.011  0.43
2020 Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Corrigendum: Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angewandte Chemie (International Ed. in English). 59: 2144. PMID 31985176 DOI: 10.1002/Anie.201915969  0.305
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. Journal of Computational Chemistry. PMID 31976572 DOI: 10.1002/Jcc.26151  0.682
2019 Lam JH, Li Y, Zhu L, Umarov R, Jiang H, Héliou A, Sheong FK, Liu T, Long Y, Li Y, Fang L, Altman RB, Chen W, Huang X, Gao X. A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature Communications. 10: 4941. PMID 31666519 DOI: 10.1038/S41467-019-12920-0  0.643
2019 Tu Y, Yu Y, Zhou Z, Xie S, Yao B, Guan S, Situ B, Liu Y, Kwok RTK, Lam JWY, Chen S, Huang X, Zeng Z, Tang BZ. Specific and quantitative detection of albumin in biological fluids by tetrazolate-functionalized water-soluble AIEgens. Acs Applied Materials & Interfaces. PMID 31340641 DOI: 10.1021/Acsami.9B10359  0.767
2019 Zhao Z, Zheng X, Du L, Xiong Y, He W, Gao X, Li C, Liu Y, Xu B, Zhang J, Song F, Yu Y, Zhao X, Cai Y, He X, ... ... Huang X, et al. Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process. Nature Communications. 10: 2952. PMID 31273202 DOI: 10.1038/S41467-019-10818-5  0.521
2019 Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PP, Wang D, Zhang Y, Huang X. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Nature Energy. 2: 228-235. PMID 31179024 DOI: 10.1038/S41929-019-0227-5  0.367
2019 Wang L, Chen J, Zeng X, Cheung PP, Zheng X, Xie L, Shi X, Ren L, Huang X, Wang Y. Mechanistic Insights and Rational Design of a Versatile Surface with Cells/Bacteria Recognition Capability via Orientated Fusion Peptides. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 6: 1801827. PMID 31065519 DOI: 10.1002/Advs.201801827  0.503
2019 Hsieh ST, Zhang L, Ye DW, Huang X, Cheng YC. A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways. Faraday Discussions. PMID 31016302 DOI: 10.1039/C8Fd00205C  0.329
2019 Zhu L, Sheong FK, Cao S, Liu S, Unarta IC, Huang X. TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules. The Journal of Chemical Physics. 150: 124105. PMID 30927873 DOI: 10.1063/1.5082633  0.684
2019 Konovalov KA, Pardo-Avila F, Tse CKM, 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. The Journal of Biological Chemistry. PMID 30718278 DOI: 10.1074/Jbc.Ra118.007333  0.385
2018 Konovalov KA, Wang W, Huang X. Conformational selection turns on phenylalanine hydroxylase. The Journal of Biological Chemistry. 293: 19544-19545. PMID 30578407 DOI: 10.1074/Jbc.H118.006676  0.358
2018 Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. Journal of the American Chemical Society. PMID 30412395 DOI: 10.1021/Jacs.8B09277  0.323
2018 Wang W, Liang T, Sheong FK, Fan X, Huang X. An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling. The Journal of Chemical Physics. 149: 072337. PMID 30134698 DOI: 10.1063/1.5027001  0.411
2018 Zeng X, Li ZW, Zheng X, Zhu L, Sun ZY, Lu ZY, Huang X. Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways. Physical Chemistry Chemical Physics : Pccp. PMID 29620122 DOI: 10.1039/C8Cp00522B  0.711
2018 Zeng X, Zhu L, Zheng X, Cecchini M, Huang X. Harnessing complexity in molecular self-assembly using computer simulations. Physical Chemistry Chemical Physics : Pccp. PMID 29479585 DOI: 10.1039/C7Cp06181A  0.72
2018 Unarta IC, Zhu L, Tse CKM, Cheung PP, Yu J, Huang X. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Current Opinion in Structural Biology. 49: 54-62. PMID 29414512 DOI: 10.1016/J.Sbi.2018.01.002  0.636
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 Chinese Journal of Chemical Physics. 31: 404-420. DOI: 10.1063/1674-0068/31/Cjcp1806147  0.758
2017 Bratkowski M, Unarta IC, Zhu L, Shubbar M, Huang X, Liu X. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator crosstalk. The Journal of Biological Chemistry. PMID 29158257 DOI: 10.1074/Jbc.M117.811521  0.638
2017 Zhang H, Zheng X, Xie N, He Z, Liu J, Leung NLC, Niu Y, Huang X, Wong KS, Kwok RTK, Sung HHY, Williams ID, Qin A, Lam JWY, Tang BZ. Why do simple molecules with "isolated" phenyl rings emit visible light? Journal of the American Chemical Society. PMID 29064249 DOI: 10.1021/Jacs.7B08592  0.515
2017 Meng L, Sheong FK, Zeng X, Zhu L, Huang X. Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems. The Journal of Chemical Physics. 147: 044112. PMID 28764388 DOI: 10.1063/1.4995558  0.749
2017 Peng HQ, Zheng X, Han T, Kwok RTK, Lam JWY, Huang X, Tang BZ. Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers. Journal of the American Chemical Society. PMID 28692263 DOI: 10.1021/Jacs.7B05792  0.518
2017 Jiang L, Cao S, Cheung PP, Zheng X, Leung CWT, Peng Q, Shuai Z, Tang BZ, Yao S, Huang X. Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect. Nature Communications. 8: 15639. PMID 28561067 DOI: 10.1038/Ncomms15639  0.672
2017 Chen C, Song Z, Zheng X, He Z, Liu B, Huang X, Kong D, Ding D, Tang BZ. AIEgen-based theranostic system: targeted imaging of cancer cells and adjuvant amplification of antitumor efficacy of paclitaxel. Chemical Science. 8: 2191-2198. PMID 28507673 DOI: 10.1039/C6Sc03859J  0.5
2017 Zheng X, Zhu L, Zeng X, Meng L, Zhang L, Wang D, Huang X. Kinetics-Controlled Amphiphiles Self-Assembly Processes. The Journal of Physical Chemistry Letters. PMID 28365997 DOI: 10.1021/Acs.Jpclett.7B00160  0.773
2017 Weng J, Gu S, Gao X, Huang X, Wang W. Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2. Physical Chemistry Chemical Physics : Pccp. PMID 28267156 DOI: 10.1039/C6Cp07943A  0.308
2017 Zhang Q, Zheng X, Kuang G, Wang W, Zhu L, Pang R, Shi X, Shang X, Huang X, Liu PN, Lin N. Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces. The Journal of Physical Chemistry Letters. PMID 28248110 DOI: 10.1021/Acs.Jpclett.7B00007  0.723
2017 Pan X, He Y, Lei J, Huang X, Zhao Y. Crystallographic snapshots of Class A β-lactamase catalysis reveal structural changes that facilitate β-lactam hydrolysis. The Journal of Biological Chemistry. PMID 28100776 DOI: 10.1074/Jbc.M116.764340  0.327
2017 Jiang H, Zhu L, Héliou A, Gao X, Bernauer J, Huang X. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches. Methods in Molecular Biology (Clifton, N.J.). 1517: 251-275. PMID 27924488 DOI: 10.1007/978-1-4939-6563-2_18  0.635
2017 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 Molecular Physics. 116: 1003-1013. DOI: 10.1080/00268976.2017.1416195  0.629
2017 Wang W, Cao S, Zhu L, Huang X. Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules Wires Computational Molecular Science. 8. DOI: 10.1002/Wcms.1343  0.616
2016 Liu S, Zhu L, Sheong FK, Wang W, Huang X. Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories. Journal of Computational Chemistry. PMID 27868222 DOI: 10.1002/Jcc.24664  0.682
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. Physical Chemistry Chemical Physics : Pccp. PMID 27759128 DOI: 10.1039/C6Cp05590G  0.386
2016 Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angewandte Chemie (International Ed. in English). PMID 27730716 DOI: 10.1002/Anie.201606613  0.38
2016 Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X. Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. Progress in Biophysics and Molecular Biology. PMID 27697475 DOI: 10.1016/J.Pbiomolbio.2016.09.008  0.661
2016 Lin H, Chen S, Hu H, Zhang L, Ma T, Lai JY, Li Z, Qin A, Huang X, Tang B, Yan H. Reduced Intramolecular Twisting Improves the Performance of 3D Molecular Acceptors in Non-Fullerene Organic Solar Cells. Advanced Materials (Deerfield Beach, Fla.). PMID 27501996 DOI: 10.1002/Adma.201600997  0.716
2016 Zhang L, Jiang H, Sheong FK, Pardo-Avila F, Cheung PP, Huang X. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands. Methods in Enzymology. 578: 343-71. PMID 27497174 DOI: 10.1016/Bs.Mie.2016.05.026  0.376
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. PMID 27417250 DOI: 10.1039/C6Nr03599J  0.759
2016 Qiao Q, Zhang HD, Huang X. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states. The Journal of Chemical Physics. 144: 154107. PMID 27389209 DOI: 10.1063/1.4946793  0.341
2016 Zheng J, Wang L, Zeng X, Zheng X, Zhang Y, Liu S, Shi X, Wang YJ, Huang X, Ren L. Controlling the Integration of Polyvinylpyrrolidone onto Substrate by Quartz Crystal Microbalance with Dissipation to Achieve Excellent Protein Resistance and Detoxification. Acs Applied Materials & Interfaces. PMID 27363467 DOI: 10.1021/Acsami.6B04348  0.538
2016 Zhu L, Sheong FK, Zeng X, Huang X. Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models. Physical Chemistry Chemical Physics : Pccp. PMID 27314275 DOI: 10.1039/C6Cp02545E  0.681
2016 Zeng X, Li B, Qiao Q, Zhu L, Lu ZY, Huang X. Elucidating dominant pathways of the nano-particle self-assembly process. Physical Chemistry Chemical Physics : Pccp. PMID 27198654 DOI: 10.1039/C6Cp01808D  0.634
2016 Da LT, Pardo-Avila F, Xu L, Silva DA, 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. PMID 27091704 DOI: 10.1038/Ncomms11244  0.419
2016 Hwang CS, Xu L, Wang W, Ulrich S, Zhang L, Chong J, Shin JH, Huang X, Kool ET, McKenna CE, Wang D. Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Research. PMID 27060150 DOI: 10.1093/Nar/Gkw220  0.372
2016 Zhang L, Pardo-Avila F, Unarta IC, Cheung PP, Wang G, Wang D, Huang X. Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models. Accounts of Chemical Research. PMID 26991064 DOI: 10.1021/Acs.Accounts.5B00536  0.464
2016 Zhu L, Jiang H, Sheong FK, 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. The Journal of Physical Chemistry. B. PMID 26908081 DOI: 10.1021/Acs.Jpcb.5B12426  0.658
2016 Li H, Zheng X, Su H, Lam JW, Sing Wong K, Xue S, Huang X, Huang X, Li BS, Tang BZ. Synthesis, optical properties, and helical self-assembly of a bivaline-containing tetraphenylethene. Scientific Reports. 6: 19277. PMID 26758799 DOI: 10.1038/Srep19277  0.541
2015 Ablikim M, Achasov MN, Ai XC, Albayrak O, Albrecht M, Ambrose DJ, Amoroso A, An FF, An Q, Bai JZ, Ferroli RB, Ban Y, Bennett DW, Bennett JV, Bertani M, ... Huang XT, et al. Observation of a Neutral Structure near the DD[over ¯]^{*} Mass Threshold in e^{+}e^{-}→(DD[over ¯]^{*})^{0}π^{0} at sqrt[s]=4.226 and 4.257 GeV. Physical Review Letters. 115: 222002. PMID 26650295 DOI: 10.1103/Physrevlett.115.222002  0.311
2015 Ablikim M, Achasov MN, Ai XC, Albayrak O, Albrecht M, Ambrose DJ, Amoroso A, An FF, An Q, Bai JZ, Baldini Ferroli R, Ban Y, Bennett DW, Bennett JV, Bertani M, ... Huang XT, et al. Measurement of the Absolute Branching Fraction for Λ_{c}^{+}→Λe^{+}ν_{e}. Physical Review Letters. 115: 221805. PMID 26650293 DOI: 10.1103/Physrevlett.115.221805  0.322
2015 Sheong FK, Silva DA, Meng L, Zhao Y, Huang X. Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems. Journal of Chemical Theory and Computation. 11: 17-27. PMID 26574199 DOI: 10.1021/Ct5007168  0.646
2015 Ablikim M, Achasov MN, Ai XC, Albayrak O, Albrecht M, Ambrose DJ, Amoroso A, An FF, An Q, Bai JZ, Ferroli RB, Ban Y, Bennett DW, Bennett JV, Bertani M, ... Huang XT, et al. Observation of a Neutral Charmoniumlike State Z_{c}(4025)^{0} in e^{+}e^{-}→(D^{*}D[over ¯]^{*})^{0}π^{0}. Physical Review Letters. 115: 182002. PMID 26565461 DOI: 10.1103/Physrevlett.115.182002  0.315
2015 Li W, Guo Z, Jones JA, Huang X, Chen X, Liu P, Chen S, Liu H. Training of Working Memory Impacts Neural Processing of Vocal Pitch Regulation. Scientific Reports. 5: 16562. PMID 26553373 DOI: 10.1038/srep16562  0.311
2015 Su S, Duan J, Chen T, Huang X, Shang E, Yu L, Wei K, Zhu Y, Guo J, Guo S, Liu P, Qian D, Tang Y. Corrigendum: Frankincense and myrrh suppress inflammation via regulation of the metabolic profiling and the MAPK signaling pathway. Scientific Reports. 5: 15597. PMID 26513369 DOI: 10.1038/Srep15597  0.337
2015 Li B, Yuan X, Chen Y, Liu P, Huang X. Visual duration aftereffect is position invariant. Frontiers in Psychology. 6: 1536. PMID 26500591 DOI: 10.3389/fpsyg.2015.01536  0.317
2015 He C, Huang X, Liu Y, Li F, Yang Y, Tao H, Han C, Zhao C, Xiao Y, Shi Y. Structural insights on mouse L-threonine dehydrogenase: A regulatory role of Arg180 in catalysis. Journal of Structural Biology. PMID 26492815 DOI: 10.1016/J.Jsb.2015.10.014  0.505
2015 Cao S, Sheong FK, 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. The Journal of Chemical Physics. 143: 054110. PMID 26254645 DOI: 10.1063/1.4928051  0.324
2015 Jiang H, Sheong FK, 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 Computational Biology. 11: e1004404. PMID 26181723 DOI: 10.1371/Journal.Pcbi.1004404  0.662
2015 Wang E, He Z, Zhao E, Meng L, Schütt C, Lam JW, Sung HH, Williams ID, Huang X, Herges R, Tang BZ. Aggregation-Induced-Emission-Active Macrocycle Exhibiting Analogous Triply and Singly Twisted Möbius Topologies. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 26177730 DOI: 10.1002/Chem.201502224  0.606
2015 Zhang L, Silva DA, Pardo-Avila F, Wang D, Huang X. Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes. Plos Computational Biology. 11: e1004354. PMID 26134169 DOI: 10.1371/Journal.Pcbi.1004354  0.376
2015 Xu L, Wang W, Zhang L, Chong J, Huang X, Wang D. Impact of template backbone heterogeneity on RNA polymerase II transcription. Nucleic Acids Research. 43: 2232-41. PMID 25662224 DOI: 10.1093/Nar/Gkv059  0.356
2015 Liu Y, Mu C, Jiang K, Zhao J, Li Y, Zhang L, Li Z, Lai JY, Hu H, Ma T, Hu R, Yu D, Huang X, Tang BZ, Yan H. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells. Advanced Materials (Deerfield Beach, Fla.). 27: 1015-20. PMID 25429918 DOI: 10.1002/Adma.201404152  0.307
2015 Zhao E, Lam JWY, Meng L, Hong Y, Deng H, Bai G, Huang X, Hao J, Tang BZ. Poly[(maleic anhydride)-alt-(vinyl acetate)]: A pure oxygenic nonconjugated macromolecule with strong light emission and solvatochromic effect Macromolecules. 48: 64-71. DOI: 10.1021/Ma502160W  0.55
2014 Yu J, Da LT, Huang X. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Physical Biology. 12: 016004. PMID 25475208 DOI: 10.1088/1478-3975/12/1/016004  0.388
2014 Gu S, Silva DA, Meng L, Yue A, Huang X. Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis. Plos Computational Biology. 10: e1003767. PMID 25101697 DOI: 10.1371/Journal.Pcbi.1003767  0.644
2014 Xu L, Zhang L, Chong J, Xu J, Huang X, Wang D. Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity. Proceedings of the National Academy of Sciences of the United States of America. 111: E3269-76. PMID 25074911 DOI: 10.1073/Pnas.1406234111  0.357
2014 Zhang L, Silva DA, Zhang H, Yue A, Yan Y, Huang X. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre. Nature Communications. 5: 4170. PMID 24954746 DOI: 10.1038/Ncomms5170  0.346
2014 Silva DA, Weiss DR, Pardo Avila F, Da LT, Levitt M, Wang D, Huang X. Millisecond dynamics of RNA polymerase II translocation at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 111: 7665-70. PMID 24753580 DOI: 10.1073/Pnas.1315751111  0.71
2014 Da LT, Sheong FK, Silva DA, Huang X. Application of Markov State Models to simulate long timescale dynamics of biological macromolecules. Advances in Experimental Medicine and Biology. 805: 29-66. PMID 24446356 DOI: 10.1007/978-3-319-02970-2_2  0.431
2014 Huang X, De Fabritiis G. Understanding molecular recognition by kinetic network models constructed from molecular dynamics simulations. Advances in Experimental Medicine and Biology. 797: 107-14. PMID 24297279 DOI: 10.1007/978-94-007-7606-7_9  0.392
2013 Bowman GR, Meng L, Huang X. Quantitative comparison of alternative methods for coarse-graining biological networks. The Journal of Chemical Physics. 139: 121905. PMID 24089717 DOI: 10.1063/1.4812768  0.712
2013 Qiao Q, Bowman GR, Huang X. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. Journal of the American Chemical Society. 135: 16092-101. PMID 24021023 DOI: 10.1021/Ja403147M  0.627
2013 Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics. The Journal of Chemical Physics. 138: 174106. PMID 23656113 DOI: 10.1063/1.4802007  0.621
2013 Da LT, Pardo Avila F, Wang D, Huang X. A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. Plos Computational Biology. 9: e1003020. PMID 23592966 DOI: 10.1371/Journal.Pcbi.1003020  0.402
2013 Zhao Y, Sheong FK, Sun J, Sander P, Huang X. A fast parallel clustering algorithm for molecular simulation trajectories. Journal of Computational Chemistry. 34: 95-104. PMID 22996151 DOI: 10.1002/Jcc.23110  0.322
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 Journal of Theoretical and Computational Chemistry. 12: 1341005. DOI: 10.1142/S0219633613410058  0.351
2012 Song J, Gao F, Cui RZ, Shuang F, Liang W, Huang X, Zhuang W. Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation. The Journal of Physical Chemistry. B. 116: 12669-76. PMID 22994891 DOI: 10.1021/Jp304714Q  0.315
2012 Zhang L, Silva DA, Yan Y, Huang X. Force field development for cofactors in the photosystem II. Journal of Computational Chemistry. 33: 1969-80. PMID 22685077 DOI: 10.1002/Jcc.23016  0.336
2012 Flores SC, Bernauer J, Shin S, Zhou R, Huang X. Multiscale modeling of macromolecular biosystems. Briefings in Bioinformatics. 13: 395-405. PMID 22228511 DOI: 10.1093/Bib/Bbr077  0.542
2012 Da LT, Wang D, Huang X. Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. Journal of the American Chemical Society. 134: 2399-406. PMID 22206270 DOI: 10.1021/Ja210656K  0.394
2012 Hong Y, Meng L, Chen S, Leung CW, Da LT, Faisal M, Silva DA, Liu J, Lam JW, Huang X, Tang BZ. Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics. Journal of the American Chemical Society. 134: 1680-9. PMID 22191699 DOI: 10.1021/Ja208720A  0.595
2012 Z. Cui R, Silva D, Song J, R. Bowman G, Zhuang W, Huang X. Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics Current Physical Chemistry. 2: 45-58. DOI: 10.2174/1877946811202010045  0.395
2012 Liu J, Su H, Meng L, Zhao Y, Deng C, Ng JCY, Lu P, Faisal M, Lam JWY, Huang X, Wu H, Wong KS, Tang BZ. What makes efficient circularly polarised luminescence in the condensed phase: aggregation-induced circular dichroism and light emission Chemical Science. 3: 2737. DOI: 10.1039/C2Sc20382K  0.621
2011 Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD. Initiation complex structure and promoter proofreading. Science (New York, N.Y.). 333: 633-7. PMID 21798951 DOI: 10.1126/Science.1206629  0.314
2011 Silva DA, Bowman GR, Sosa-Peinado A, Huang X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. Plos Computational Biology. 7: e1002054. PMID 21637799 DOI: 10.1371/Journal.Pcbi.1002054  0.608
2011 Bernauer J, Huang X, Sim AY, Levitt M. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. Rna (New York, N.Y.). 17: 1066-75. PMID 21521828 DOI: 10.1261/Rna.2543711  0.496
2011 Zhuang W, Cui RZ, Silva DA, Huang X. Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach. The Journal of Physical Chemistry. B. 115: 5415-24. PMID 21388153 DOI: 10.1021/Jp109592B  0.364
2010 Huang X, Wang D, Weiss DR, Bushnell DA, Kornberg RD, Levitt M. RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proceedings of the National Academy of Sciences of the United States of America. 107: 15745-50. PMID 20798057 DOI: 10.1073/Pnas.1009898107  0.726
2010 Wang D, Zhu G, Huang X, Lippard SJ. X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct. Proceedings of the National Academy of Sciences of the United States of America. 107: 9584-9. PMID 20448203 DOI: 10.1073/Pnas.1002565107  0.353
2010 Bowman GR, Huang X, Pande VS. Network models for molecular kinetics and their initial applications to human health. Cell Research. 20: 622-30. PMID 20421891 DOI: 10.1038/Cr.2010.57  0.673
2010 Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ. Dewetting transitions in protein cavities. Proteins. 78: 1856-69. PMID 20225258 DOI: 10.1002/Prot.22699  0.753
2010 Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS. Constructing multi-resolution markov state models (MSMS) to elucidate RNA hairpin folding mechanisms Pacific Symposium On Biocomputing 2010, Psb 2010. 228-239. PMID 19908375  0.665
2009 Huang X, Bowman GR, Bacallado S, Pande VS. Rapid equilibrium sampling initiated from nonequilibrium data. Proceedings of the National Academy of Sciences of the United States of America. 106: 19765-9. PMID 19805023 DOI: 10.1073/Pnas.0909088106  0.679
2009 Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science (New York, N.Y.). 324: 1203-6. PMID 19478184 DOI: 10.1126/Science.1168729  0.505
2009 Bowman GR, Huang X, Pande VS. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (San Diego, Calif.). 49: 197-201. PMID 19410002 DOI: 10.1016/J.Ymeth.2009.04.013  0.681
2009 Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, Carlsson G. Topological methods for exploring low-density states in biomolecular folding pathways. The Journal of Chemical Physics. 130: 144115. PMID 19368437 DOI: 10.1063/1.3103496  0.688
2009 Kelley NW, Huang X, Tam S, Spiess C, Frydman J, Pande VS. The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. Journal of Molecular Biology. 388: 919-27. PMID 19361448 DOI: 10.1016/J.Jmb.2009.01.032  0.551
2009 Bowman GR, Huang X, Pande VS. Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales Biophysical Journal. 96: 575a. DOI: 10.1016/J.Bpj.2008.12.3002  0.698
2008 Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS. Structural insight into RNA hairpin folding intermediates. Journal of the American Chemical Society. 130: 9676-8. PMID 18593120 DOI: 10.1021/Ja8032857  0.693
2008 Hu Z, Huang X, Annapureddy HV, Margulis CJ. Molecular dynamics study of the temperature-dependent Optical Kerr effect spectra and intermolecular dynamics of room temperature ionic liquid 1-methoxyethylpyridinium dicyanoamide. The Journal of Physical Chemistry. B. 112: 7837-49. PMID 18537285 DOI: 10.1021/Jp800729G  0.644
2008 Huang X, Bowman GR, Pande VS. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. The Journal of Chemical Physics. 128: 205106. PMID 18513049 DOI: 10.1063/1.2908251  0.667
2007 Hua L, Huang X, Liu P, Zhou R, Berne BJ. Nanoscale dewetting transition in protein complex folding. The Journal of Physical Chemistry. B. 111: 9069-77. PMID 17608515 DOI: 10.1021/Jp0704923  0.79
2007 Huang X, Hagen M, Kim B, Friesner RA, Zhou R, Berne BJ. Replica exchange with solute tempering: efficiency in large scale systems. The Journal of Physical Chemistry. B. 111: 5405-10. PMID 17439169 DOI: 10.1021/Jp068826W  0.741
2006 Liu P, Huang X, Zhou R, Berne BJ. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. The Journal of Physical Chemistry. B. 110: 19018-22. PMID 16986898 DOI: 10.1021/Jp060365R  0.691
2006 Hua L, Huang X, Zhou R, Berne BJ. Dynamics of water confined in the interdomain region of a multidomain protein. The Journal of Physical Chemistry. B. 110: 3704-11. PMID 16494427 DOI: 10.1021/Jp055399Y  0.775
2005 Huang X, Zhou R, Berne BJ. Drying and hydrophobic collapse of paraffin plates. The Journal of Physical Chemistry. B. 109: 3546-52. PMID 16851392 DOI: 10.1021/Jp045520L  0.65
2005 Huang X, Margulis CJ, Li Y, Berne BJ. 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(-)]. Journal of the American Chemical Society. 127: 17842-51. PMID 16351115 DOI: 10.1021/Ja055315Z  0.657
2005 Liu P, Huang X, Zhou R, Berne BJ. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature. 437: 159-62. PMID 16136146 DOI: 10.1038/Nature03926  0.691
2004 Zhou R, Huang X, Margulis CJ, Berne BJ. Hydrophobic collapse in multidomain protein folding. Science (New York, N.Y.). 305: 1605-9. PMID 15361621 DOI: 10.1126/Science.1101176  0.752
2004 Huang X, Margulis CJ, Berne BJ. Reply to the comment on "do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces? Journal of Physical Chemistry B. 108: 9373-9374. DOI: 10.1021/Jp040154R  0.674
2003 Huang X, Margulis CJ, Berne BJ. Dewetting-induced collapse of hydrophobic particles. Proceedings of the National Academy of Sciences of the United States of America. 100: 11953-8. PMID 14507993 DOI: 10.1073/Pnas.1934837100  0.693
2003 Huang X, Margulis CJ, Berne BJ. Do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces? Journal of Physical Chemistry B. 107: 11742-11748. DOI: 10.1021/Jp030652K  0.698
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