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, Fangqiang
The journal of physical chemistry. B, December 29, 2016. | Journal Article
2015
Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter.
Song, Hyun Deok and Zhu, Fangqiang
PloS one, vol. 10, (no. 7), pp. e0133388, 2015. | Journal Article
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 scattering
Wu, 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, Kaili
Nano Research, vol. 8, (no. 1), pp. 303-319, Jan 2015. | Journal Article
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 scattering
Wu, 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, Kaili
Nano Research, vol. 8, (no. 8), pp. 2721-2732, Aug 2015. | Journal Article
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, Fangqiang
Biophysical journal, vol. 106, (no. 6), pp. 1229-30, 2014/Mar/18. | Journal Article
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, Fangqiang
Biophysical journal, vol. 104, (no. 2), pp. 368-76, 2013/Jan/22. | Journal Article
Conformational dynamics of a ligand-free adenylate kinase.
Song, Hyun D and Zhu, Fangqiang
PloS one, vol. 8, (no. 7), pp. e68023, 2013. | Journal Article
2012
Convergence and error estimation in free energy calculations using the weighted histogram analysis method.
Zhu, Fangqiang and Hummer, Gerhard
Journal of computational chemistry, vol. 33, (no. 4), pp. 453-65, 2012/Feb/5. | Journal Article
Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.
Zhu, Fangqiang and Hummer, Gerhard
Biophysical journal, vol. 103, (no. 2), pp. 219-27, 2012/Jul/18. | Journal Article
Theory and simulation of ion conduction in the pentameric GLIC channel.
Zhu, Fangqiang and Hummer, Gerhard
Journal of chemical theory and computation, vol. 8, (no. 10), pp. 3759-3768, October 9, 2012. | Journal Article
2011
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water.
Melillo, Matthew⋅Zhu, Fangqiang⋅Snyder, Mark A and Mittal, Jeetain
The journal of physical chemistry letters, vol. 2, (no. 23), pp. 2978-2983, October 28, 2011. | Journal Article
2010
Pore opening and closing of a pentameric ligand-gated ion channel.
Zhu, Fangqiang and Hummer, Gerhard
Proceedings of the National Academy of Sciences of the United States of America, vol. 107, (no. 46), pp. 19814-9, 2010/Nov/16. | Journal Article
2009
A self-organizing algorithm for modeling protein loops.
Liu, Pu⋅Zhu, Fangqiang⋅Rassokhin, Dmitrii N and Agrafiotis, Dimitris K
PLoS computational biology, vol. 5, (no. 8), pp. e1000478, 2009/Aug. | Journal Article
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, Gerhard
Biophysical journal, vol. 97, (no. 9), pp. 2456-63, 2009/Nov/4. | Journal Article
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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