35 Publications (Page 1 of 2)
2017
Structural Model of the Tubular Assembly of the Rous Sarcoma Virus Capsid Protein.Jeon, Jaekyun⋅Qiao, Xin⋅Hung, Ivan⋅Mitra, Alok K⋅Desfosses, Ambroise⋅Huang, Daniel⋅Gor'kov, Peter L⋅Craven, Rebecca C⋅Kingston, Richard L⋅Gan, Zhehong⋅Zhu, Fangqiang and Chen, BoJournal of the American Chemical Society, vol. 139, (no. 5), pp. 2006-2013, February 8, 2017.
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2016
Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter.Song, Hyun Deok and Zhu, FangqiangThe journal of physical chemistry. B, December 29, 2016.
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2015
Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter.Song, Hyun Deok and Zhu, FangqiangPloS one, vol. 10, (no. 7), pp. e0133388, 2015.
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Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution.Qiao, Xin⋅Jeon, Jaekyun⋅Weber, Jeff⋅Zhu, Fangqiang and Chen, BoData in brief, vol. 5, pp. 506-512, December 2015.
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Interface dipole enhancement effect and enhanced Rayleigh scatteringWu, Wenyun⋅Yue, Jingying⋅Li, Dongqi⋅Lin, Xiaoyang⋅Zhu, Fangqiang⋅Yin, Xue⋅Zhu, Jun⋅Dai, Xingcan⋅Liu, Peng⋅Wei, Yang⋅Wang, Jiaping⋅Yang, Haitao⋅Zhang, Lina⋅Li, Qunqing⋅Fan, Shoushan and Jiang, KailiNano Research, vol. 8, (no. 1), pp. 303-319, Jan 2015.
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Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model.Qiao, Xin⋅Jeon, Jaekyun⋅Weber, Jeff⋅Zhu, Fangqiang and Chen, BoBiochimica et biophysica acta, vol. 1850, (no. 11), pp. 2353-2367, November 2015.
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Monte Carlo Simulations of HIV Capsid Protein Homodimer.Zhu, Fangqiang and Chen, BoJournal of chemical information and modeling, vol. 55, (no. 7), pp. 1361-1368, July 27, 2015.
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True-color real-time imaging and spectroscopy of carbon nanotubes on substrates using enhanced Rayleigh scatteringWu, Wenyun⋅Yue, Jingying⋅Lin, Xiaoyang⋅Li, Dongqi⋅Zhu, Fangqiang⋅Yin, Xue⋅Zhu, Jun⋅Wang, Jiangtao⋅Zhang, Jin⋅Chen, Yuan⋅Wang, Xinhe⋅Li, Tianyi⋅He, Yujun⋅Dai, Xingcan⋅Liu, Peng⋅Wei, Yang⋅Wang, Jiaping⋅Zhang, Wei⋅Huang, Yidong⋅Fan, Li⋅Zhang, Lina⋅Li, Qunqing⋅Fan, Shoushan and Jiang, KailiNano Research, vol. 8, (no. 8), pp. 2721-2732, Aug 2015.
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2014
Evaluating membrane affinity by integrating protein orientations.Zhu, Fangqiang and Clauss, MatthiasJournal of molecular graphics & modelling, vol. 54, pp. 141-147, November 2014.
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How does Water Pass through a Sugar Transporter?Zhu, FangqiangBiophysical journal, vol. 106, (no. 6), pp. 1229-30, 2014/Mar/18.
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Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos.Xue, Yi⋅Yuwen, Tairan⋅Zhu, Fangqiang and Skrynnikov, Nikolai RBiochemistry, vol. 53, (no. 41), pp. 6473-6495, October 21, 2014.
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2013
Collective diffusion model for ion conduction through microscopic channels.Liu, Yingting and Zhu, FangqiangBiophysical journal, vol. 104, (no. 2), pp. 368-76, 2013/Jan/22.
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Conformational dynamics of a ligand-free adenylate kinase.Song, Hyun D and Zhu, FangqiangPloS one, vol. 8, (no. 7), pp. e68023, 2013.
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2012
Convergence and error estimation in free energy calculations using the weighted histogram analysis method.Zhu, Fangqiang and Hummer, GerhardJournal of computational chemistry, vol. 33, (no. 4), pp. 453-65, 2012/Feb/5.
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Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.Zhu, Fangqiang and Hummer, GerhardBiophysical journal, vol. 103, (no. 2), pp. 219-27, 2012/Jul/18.
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Theory and simulation of ion conduction in the pentameric GLIC channel.Zhu, Fangqiang and Hummer, GerhardJournal of chemical theory and computation, vol. 8, (no. 10), pp. 3759-3768, October 9, 2012.
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2011
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water.Melillo, Matthew⋅Zhu, Fangqiang⋅Snyder, Mark A and Mittal, JeetainThe journal of physical chemistry letters, vol. 2, (no. 23), pp. 2978-2983, October 28, 2011.
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2010
Pore opening and closing of a pentameric ligand-gated ion channel.Zhu, Fangqiang and Hummer, GerhardProceedings of the National Academy of Sciences of the United States of America, vol. 107, (no. 46), pp. 19814-9, 2010/Nov/16.
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2009
A self-organizing algorithm for modeling protein loops.Liu, Pu⋅Zhu, Fangqiang⋅Rassokhin, Dmitrii N and Agrafiotis, Dimitris KPLoS computational biology, vol. 5, (no. 8), pp. e1000478, 2009/Aug.
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Conformational analysis of macrocycles: finding what common search methods miss.Bonnet, Pascal⋅Agrafiotis, Dimitris⋅Zhu, Fangqiang and Martin, EricJournal of chemical information and modeling, vol. 49, (no. 10), pp. 2242-59, 2009/Oct.
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Gating transition of pentameric ligand-gated ion channels.Zhu, Fangqiang and Hummer, GerhardBiophysical journal, vol. 97, (no. 9), pp. 2456-63, 2009/Nov/4.
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2007
Charge delocalization in proton channels, I: the aquaporin channels and proton blockage.Chen, Hanning⋅Ilan, Boaz⋅Wu, Yujie⋅Zhu, Fangqiang⋅Schulten, Klaus J and Voth, Gregory ABiophysical journal, vol. 92, (no. 1), pp. 46-60, 2007/Jan/1.
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Conformational Sampling of Bioactive Molecules: A Comparative StudyAgrafiotis, Dimitris⋅Gibbs, Alan C⋅Zhu, Fangqiang⋅Izrailev, Sergei and Martin, EricJournal of Chemical Information and Modeling, vol. 47, (no. 3), May 2007.
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Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an AntagonistLi, Youyong⋅Zhu, Fangqiang⋅Vaidehi, Nagarajan⋅Goddard, William A⋅Sheinerman, Felix⋅Reiling, Stephan⋅Morize, Isabelle⋅Mu, Lan⋅Harris, Keith⋅Ardati, Ali and Laoui, AbdelazizeJournal of the American Chemical Society, vol. 129, (no. 35), pp. 10720-10731, 2007.
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Recursive Distance Partitioning Algorithm for Common Pharmacophore IdentificationZhu, Fangqiang and Agrafiotis, DimitrisJournal of Chemical Information and Modeling, vol. 47, (no. 4), Jul 2007.
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