Publications

  1. Yingting Liu and Fangqiang Zhu. "Collective diffusion model for ion conduction through microscopic channels". Biophysical Journal, 104:368-376, 2013. [pdf] [journal]
  2. Fangqiang Zhu and Gerhard Hummer. "Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction". Biophysical Journal, 103:219-227, 2012. [pdf] [journal]
  3. Fangqiang Zhu and Gerhard Hummer. "Theory and simulation of ion conduction in the pentameric GLIC channel". Journal of Chemical Theory and Computation, 8:3759-3768, 2012. [pdf] [journal]
  4. Fangqiang Zhu and Gerhard Hummer. "Convergence and error estimation in free energy calculations using the weighted histogram analysis method". Journal of Computational Chemistry, 33:453-465, 2012. [pdf] [journal]
  5. Matthew Melillo, Fangqiang Zhu, Mark A. Snyder, and Jeetain Mittal. "Water transport through nanotubes with varying interaction strength between tube wall and water". The Journal of Physical Chemistry Letters, 2: 2978-2983, 2011. [journal]
  6. Dimitris K. Agrafiotis, Huafeng Xu, Fangqiang Zhu, Deepak Bandyopadhyay, and Pu Liu. "Stochastic proximity embedding: methods and applications". Molecular Informatics, 29:758-770, 2010. [journal]
  7. Fangqiang Zhu and Gerhard Hummer. "Pore opening and closing of a pentameric ligand-gated ion channel". Proceedings of the National Academy of Sciences USA (edited by J.-P. Changeux), 107:19814-19819, 2010. [pdf] [journal]
  8. Fangqiang Zhu and Gerhard Hummer. "Gating transition of pentameric ligand-gated ion channels". Biophysical Journal, 97:2456-63, 2009. [pdf] [journal]
  9. Pascal Bonnet, Dimitris K. Agrafiotis, Fangqiang Zhu, and Eric Martin. "Conformational analysis of macrocycles: finding what common search methods miss". Journal of Chemical Information and Modeling, 49:2242-2259, 2009. [journal]
  10. Pu Liu, Fangqiang Zhu, Dmitrii N. Rassokhin, and Dimitris K. Agrafiotis. "A self-organizing algorithm for modeling protein loops". PLoS Computational Biology, 5:e1000478, 2009. [journal]
  11. Youyong Li, Fangqiang Zhu, Nagarajan Vaidehi, William A. Goddard III, Felix Sheinerman, Stephan Reiling, Isabelle Morize, Lan Mu, Keith Harris, Ali Ardati, and Abdelazize Laoui. "Prediction of the 3D structure and dynamics of human DP G-Protein coupled receptor bound to an agonist and an antagonist". Journal of the American Chemical Society, 129:10720-10731, 2007. [journal]
  12. Fangqiang Zhu and Dimitris K. Agrafiotis. "Recursive distance partitioning algorithm for common pharmacophore identification". Journal of Chemical Information and Modeling, 47:1619-1625, 2007. [pdf] [journal]
  13. Dimitris K. Agrafiotis, Alan Gibbs, Fangqiang Zhu, Sergei Izrailev, and Eric Martin. "Conformational sampling of bioactive molecules: a comparative study". Journal of Chemical Information and Modeling, 47:1067-1086, 2007. [journal]
  14. Fangqiang Zhu and Dimitris K. Agrafiotis. "Self-organizing superimposition algorithm for conformational sampling". Journal of Computational Chemistry, 28:1234-1239, 2007. [pdf] [journal]
  15. Hanning Chen, Boaz Ilan, Yujie Wu, Fangqiang Zhu, Klaus Schulten, and Gregory A. Voth. "Charge delocalization in proton channels. I. The aquaporin channels and proton blockage". Biophysical Journal, 92:46-60, 2007. [link]
  16. Dimitris K. Agrafiotis, Alan Gibbs, Fangqiang Zhu, Sergei Izrailev, and Eric Martin. "Conformational boosting". Australian Journal of Chemistry, 59:874-878, 2006. [journal]
  17. Sergei Izrailev, Fangqiang Zhu, and Dimitris K. Agrafiotis. "A distance geometry heuristic for expanding the range of geometries sampled during conformational search". Journal of Computational Chemistry, 27:1962-1969, 2006. [journal]
  18. Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten. "Kinetic theory and simulation of single-channel water transport". In S. Yip, editor, Handbook of Materials Modeling, Vol. I: Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005. [link]
  19. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. "Collective diffusion model for water permeation through microscopic channels". Physical Review Letters, 93:224501, 2004. [pdf] [link]
  20. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. "Theory and simulation of water permeation in aquaporin-1". Biophysical Journal, 86:50-57, 2004. [pdf] [link]
  21. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. "Large scale simulation of protein mechanics and function". In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003. [link]
  22. Fangqiang Zhu and Klaus Schulten. "Water and proton conduction through carbon nanotubes as models for biological channels". Biophysical Journal, 85:236-244, 2003. [pdf] [link]
  23. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. "Pressure-induced water transport in membrane channels studied by molecular dynamics". Biophysical Journal, 83:154-160, 2002. [pdf] [link]
  24. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. "Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer". FEBS Letters, 504:212-218, 2001. [pdf] [link]
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