Fangqiang Zhu

发表

Collective diffusion model for water permeation through microscopic channels.

K. Schulten, Fangqiang Zhu, E. Tajkhorshid, 2004, Physical review letters.

Pressure-induced water transport in membrane channels studied by molecular dynamics.

K. Schulten, Fangqiang Zhu, E. Tajkhorshid, 2002, Biophysical journal.

Molecular dynamics study of aquaporin‐1 water channel in a lipid bilayer

K. Schulten, Fangqiang Zhu, E. Tajkhorshid, 2001, FEBS letters.

Theory and simulation of water permeation in aquaporin-1.

K. Schulten, Fangqiang Zhu, E. Tajkhorshid, 2004, Biophysical journal.

Stochastic Proximity Embedding: Methods and Applications

Pu Liu, Huafeng Xu, Deepak Bandyopadhyay, 2010, Molecular informatics.

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.

Fangqiang Zhu, N. Skrynnikov, Yi Xue, 2014, Biochemistry.

Conformational Dynamics of a Ligand-Free Adenylate Kinase

Fangqiang Zhu, H. Song, 2013, PloS one.

Structural Model of the Tubular Assembly of the Rous Sarcoma Virus Capsid Protein.

Fangqiang Zhu, Daniel Huang, A. Mitra, 2017, Journal of the American Chemical Society.

Charge delocalization in proton channels, I: the aquaporin channels and proton blockage.

Klaus Schulten, Gregory A Voth, Yujie Wu, 2007, Biophysical journal.

Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water.

Jeetain Mittal, Fangqiang Zhu, Fangqiang Zhu, 2011, The journal of physical chemistry letters.

Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts.

Fangqiang Zhu, Hamed Meshkin, 2017, Journal of chemical theory and computation.

Evaluating membrane affinity by integrating protein orientations.

Fangqiang Zhu, M. Clauss, 2014, Journal of molecular graphics & modelling.

Large-scale application of free energy perturbation calculations for antibody design

A. Zemla, Fangqiang Zhu, D. Faissol, 2022, Scientific Reports.

How does water pass through a sugar transporter?

Fangqiang Zhu, 2014, Biophysical journal.

Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays

Fangqiang Zhu, F. Lightstone, H. Ingólfsson, 2020, Journal of medicinal chemistry.

Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.

G. Hummer, Fangqiang Zhu, 2012, Biophysical journal.

Large scale simulation of protein mechanics and function.

Barry Isralewitz, James C. Phillips, Klaus Schulten, 2003, Advances in protein chemistry.

Pore opening and closing of a pentameric ligand-gated ion channel

Gerhard Hummer, Fangqiang Zhu, G. Hummer, 2010, Proceedings of the National Academy of Sciences.

Vitamin E Has Reduced Affinity for a Polyunsaturated Phospholipid: An Umbrella Sampling Molecular Dynamics Simulations Study.

Fangqiang Zhu, S. Wassall, Xiaoling Leng, 2018, The journal of physical chemistry. B.

Gating transition of pentameric ligand-gated ion channels.

Gerhard Hummer, Fangqiang Zhu, G. Hummer, 2009, Biophysical journal.

Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model.

Fangqiang Zhu, Jaekyun Jeon, Xin Qiao, 2015, Biochimica et biophysica acta.

Toward Convergence in Free Energy Calculations for Protein Conformational Changes: A Case Study on the Thin Gate of Mhp1 Transporter.

Fangqiang Zhu, Hamed Meshkin, 2021, Journal of chemical theory and computation.

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

Brenden K. Petersen, Edwin A. Saada, A. Zemla, 2022, bioRxiv.

Interface dipole enhancement effect and enhanced Rayleigh scattering

Fangqiang Zhu, K. Jiang, Jiaping Wang, 2014, Nano Research.

Binding Affinity Prediction by Pairwise Function Based on Neural Network

Derek Jones, Jonathan Allen, Felice C Lightstone, 2020, J. Chem. Inf. Model..

Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss

Eric J. Martin, Dimitris K. Agrafiotis, Pascal Bonnet, 2009, J. Chem. Inf. Model..

Kinetic mechanism for water in vibrating carbon nanotubes

Fangqiang Zhu, Xiaoyan Zhou, 2018, Physical Review E.

Water and proton conduction through carbon nanotubes as models for biological channels.

Klaus Schulten, Fangqiang Zhu, K. Schulten, 2003, Biophysical journal.

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

Gerhard Hummer, Fangqiang Zhu, G. Hummer, 2012, J. Comput. Chem..

Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist.

Abdelazize Laoui, Stephan Reiling, Lan Mu, 2007, Journal of the American Chemical Society.

Theory and simulation of ion conduction in the pentameric GLIC channel.

Gerhard Hummer, Fangqiang Zhu, G. Hummer, 2012, Journal of chemical theory and computation.

Monte Carlo Simulations of HIV Capsid Protein Homodimer

Bo Chen, Fangqiang Zhu, Bo Chen, 2015, J. Chem. Inf. Model..

True-color real-time imaging and spectroscopy of carbon nanotubes on substrates using enhanced Rayleigh scattering

Fangqiang Zhu, Yidong Huang, K. Jiang, 2015, Nano Research.

High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models

Stewart He, Adam Zemla, Felice C. Lightstone, 2021, SC21: International Conference for High Performance Computing, Networking, Storage and Analysis.

A Self-Organizing Algorithm for Modeling Protein Loops

Pu Liu, Dimitris K. Agrafiotis, Dmitrii N. Rassokhin, 2009, PLoS Comput. Biol..

Kinetic Theory and Simulation of Single-Channel Water Transport

Klaus Schulten, Fangqiang Zhu, Emad Tajkhorshid, 2005 .

Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution

Fangqiang Zhu, Xin Qiao, Bo Chen, 2015, Data in brief.

Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter

Fangqiang Zhu, H. Song, 2015, PloS one.

Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein

Fangqiang Zhu, Hao Sha, Fangqiang Zhu, 2017, J. Chem. Inf. Model..

Collective diffusion model for ion conduction through microscopic channels.

Fangqiang Zhu, Yingting Liu, 2013, Biophysical journal.

Self‐organizing superimposition algorithm for conformational sampling

Dimitris K. Agrafiotis, Fangqiang Zhu, D. Agrafiotis, 2007, J. Comput. Chem..

A distance geometry heuristic for expanding the range of geometries sampled during conformational search

Dimitris K. Agrafiotis, Fangqiang Zhu, Sergei Izrailev, 2006, J. Comput. Chem..

Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model.

Fangqiang Zhu, Xin Qiao, Bo Chen, 2015, Biochimica et biophysica acta.

Conformational Sampling of Bioactive Molecules: A Comparative Study

Eric J. Martin, Dimitris K. Agrafiotis, Alan C. Gibbs, 2007, J. Chem. Inf. Model..