Lili Duan

发表

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

Mengxin Li, Y. Cong, Yuchen Li, 2019, Front. Chem..

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

Tingjun Hou, Peichen Pan, Huiyong Sun, 2018, Physical chemistry chemical physics : PCCP.

Quantum study of HIV-1 protease-bridge water interaction.

J. H. Zhang, Lili Duan, Y. Mei, 2007, The Journal of chemical physics.

QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

Ye Mei, John Z. H. Zhang, J. H. Zhang, 2009 .

Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds.

Ye Mei, John Z H Zhang, J. H. Zhang, 2010, Journal of the American Chemical Society.

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

J. H. Zhang, Y. Cong, Yuchen Li, 2019, Front. Chem..

Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

Lili Duan, Qing G. Zhang, Guoqiang Feng, 2016, Scientific Reports.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

Ye Mei, John Z H Zhang, Ya Gao, 2012, The journal of physical chemistry. B.

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding.

J. H. Zhang, Y. Cong, Yuchen Li, 2020, Nanoscale.

Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method.

Susu Zhong, Lili Duan, Kaifang Huang, 2020, Physical chemistry chemical physics : PCCP.

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor

J. H. Zhang, Y. Cong, Lili Duan, 2020, Journal of biomolecular structure & dynamics.

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction

Huiyong Sun, John Z. H. Zhang, J. H. Zhang, 2018, Structural dynamics.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

John Z. H. Zhang, J. H. Zhang, Lili Duan, 2016, Journal of the American Chemical Society.

Study on the Amyloid Aβ42 with Accelerated Molecular Dynamics Simulations

Susu Zhong, Hao Li, Lili Duan, 2019, Communications in Theoretical Physics.

Folding of EK peptide and its dependence on salt concentration and pH: A computational study

J. H. Zhang, Dawei Zhang, Lili Duan, 2011 .

Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field

J. H. Zhang, Y. Cong, Yuchen Li, 2018, Front. Chem..

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

J. H. Zhang, Lili Duan, T. Zhu, 2017, Scientific Reports.

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy.

J. H. Zhang, Y. Cong, Susu Zhong, 2019, Physical chemistry chemical physics : PCCP.

Electronic polarization stabilizes tertiary structure prediction of HP-36

J. H. Zhang, Lili Duan, T. Zhu, 2014, Journal of Molecular Modeling.

Protein's native structure is dynamically stabilized by electronic polarization

J. H. Zhang, Lili Duan, Y. Mei, 2014 .

Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field

Mengxin Li, Y. Cong, Yuchen Li, 2017, Scientific Reports.

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity.

J. H. Zhang, Y. Cong, Susu Zhong, 2020, Nanoscale.

Using chemo-drugs or irradiation to break immune tolerance and facilitate immunotherapy in solid cancer.

Lili Duan, Yuping Sun, Aiqin Gao, 2015, Cellular immunology.

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

J. H. Zhang, Lili Duan, T. Zhu, 2013, Journal of Molecular Modeling.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

J. H. Zhang, Lili Duan, C. Ji, 2017, Physical chemistry chemical physics : PCCP.

The collision energy effect on the stereodynamics of the Ca + HCl→CaCl + H reaction

Lili Duan, Chuanlu Yang, Qinggang Zhang, 2013 .

Effect of the reagent vibration on stereodynamics of the reaction Ca + HCl → CaCl + H

Lili Duan, Chuanlu Yang, Q. Zhang, 2012 .

Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy.

J. H. Zhang, Yun Xiang, Lili Duan, 2010, Physical chemistry chemical physics : PCCP.

Difference in the binding mechanisms of ABT-263/43b with Bcl-xL/Bcl-2: computational perspective on the accurate binding free energy analysis

Hao Li, Lili Duan, Shuheng Dong, 2021, Journal of Molecular Modeling.

Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax.

J. H. Zhang, Y. Cong, Lili Duan, 2021, Physical chemistry chemical physics : PCCP.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation

Xiao He, Ye Mei, Ya Gao, 2013, Journal of Molecular Modeling.

Antiferromagnetic ferroelastic multiferroics in single-layer VOX (X = Cl, Br) predicted from first-principles

Lili Duan, Baibiao Huang, Ying Dai, 2021, Applied Physics Letters.

A numerically stable restrained electrostatic potential charge fitting method

Ye Mei, John Z. H. Zhang, Juan Zeng, 2013, J. Comput. Chem..

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix.

Ye Mei, John Z H Zhang, Ya Gao, 2012, The journal of physical chemistry. B.

Theoretical investigating mechanisms of drug-resistance generated by mutation-induced changes in influenza viruses

Lili Duan, Yihui Wang, Song Luo, 2021, Chinese Journal of Chemical Physics.

nhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations.

J. H. Zhang, Y. Cong, Lili Duan, 2021, Nanoscale.

Energetics of protein backbone hydrogen bonds and their local electrostatic environment

J. H. Zhang, Lili Duan, C. Ji, 2014, Science China Chemistry.

Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy method

J. H. Zhang, Y. Cong, Lili Duan, 2021 .

Effect of electrostatic polarization and bridging water on CDK2-ligand binding affinities calculated using a highly efficient interaction entropy method.

Qinggang Zhang, Lili Duan, Guoqiang Feng, 2017, Physical chemistry chemical physics : PCCP.

Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field

Mengxin Li, Y. Cong, Yuchen Li, 2017, Scientific Reports.

Isothermal crystallization of a single polyethylene chain induced by graphene: A molecular dynamics simulation

Lili Duan, Lizhi Wang, 2012 .

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field

J. H. Zhang, Lili Duan, Jian Chen, 2018, Front. Mol. Biosci..

Binding Mechanism of Thrombin-Ligand Systems Investigated by Polarized Protein-Specific Charge Force Field and Interaction Entropy Method.

Yuchen Li, Susu Zhong, Lili Duan, 2019, The journal of physical chemistry. B.

Direct folding simulation of a long helix in explicit water

J. H. Zhang, Dawei Zhang, Lili Duan, 2013 .

Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

J. H. Zhang, Dawei Zhang, Lili Duan, 2010 .

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

J. H. Zhang, Lili Duan, Huiyong Sun, 2018, Physical chemistry chemical physics : PCCP.

Effect of electrostatic polarization and bridging water on CDK2-ligand binding affinities calculated using a highly efficient interaction entropy method.

Lili Duan, Guoqiang Feng, Xianwei Wang, 2017, Physical chemistry chemical physics : PCCP.