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Lizhe Zhu - Publications

Affiliations: 
2007-2014 Department of Chemistry University of Amsterdam, Amsterdam, Netherlands 
 2012-2018 Department of Chemistry The Hong Kong University of Science & Technology, Hong Kong 
 2018- Warshel Institute for Computational Biology The Chinese University of Hong Kong, Shenzhen, China 
Area:
Computational Chemistry and Biophysics
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26 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
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  0.439
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  0.446
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  0.542
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  0.481
2018 Mei L, Zhou Y, Zhu L, Liu C, Wu Z, Wang F, Hao G, Yu D, Yuan H, Cui Y. Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations. International Journal of Molecular Sciences. 19. PMID 29558421 DOI: 10.3390/Ijms19030916  0.374
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  0.494
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  0.426
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  0.474
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  0.636
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  0.626
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  0.49
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  0.448
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  0.421
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  0.427
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  0.522
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  0.492
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  0.424
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  0.517
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  0.475
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  0.491
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  0.496
2013 Zhu L, Bolhuis PG, Vreede J. The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions Plos Computational Biology. 9. PMID 23468603 DOI: 10.1371/Journal.Pcbi.1002913  0.676
2011 Zhu L, Frenkel D, Bolhuis PG. Role of fluctuations in ligand binding cooperativity of membrane receptors. Physical Review Letters. 106: 168103. PMID 21599417 DOI: 10.1103/Physrevlett.106.168103  0.679
2011 Zhu L, Bolhuis PG, Vreede J. Exploring Signal Transduction Mechanism of HAMP Domains via Molecular Dynamics and Metadynamics Biophysical Journal. 100: 195a. DOI: 10.1016/J.Bpj.2010.12.1281  0.677
2010 Zhu L, Bolhuis P, Vreede J. Molecular Dynamics Simulation Study of Isolated Hamp Domain Biophysical Journal. 98: 26a. DOI: 10.1016/J.Bpj.2009.12.155  0.672
2007 Werner M, Zhu L, Aurell E. Cooperative action in eukaryotic gene regulation: physical properties of a viral example. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 061909. PMID 18233871 DOI: 10.1103/Physreve.76.061909  0.481
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