段莉莉｜山东师范大学｜学者主页

期刊论文

2026

温度耦合分子动力学探测蛋白质-配体解离动力学（英文）

黄开放，张超，段莉莉，张增辉

Chinese Journal of Chemical Physics

2025

Unraveling the Structural Basis for Antibody Synergy against Escape-Resistant Nipah Virus Mutant

Jinxin Liu, Xiaole Xu, Enhao Zhang, Song Luo, John ZengHui Zhang, Lili Duan

Journal of Chemical Information and Modeling

DOI

2025

Structural Basis of SARS-CoV-2 Nsp13-Derived Peptide-Mediated NK Cell Activation

Xiaole Xu, Song Luo, Jinxin Liu, Enhao Zhang, Houde Liang, Lili Duan

Biomacromolecules

DOI

2023

Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation

Jianwen Zhang, Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang, John Z. H. Zhang

Journal of Chemical Information and Modeling

DOI

2021

甲型流感病毒突变诱发的神经氨酸酶耐药性机制理论研究（英文）

罗松，赵晓宇，王一惠，段莉莉

Chinese Journal of Chemical Physics

2021

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

Lili Duan, Shuheng Dong, Kaifang Huang, Yalong Cong, Song Luo, John Z. H. Zhang

Physical Chemistry Chemical Physics

DOI

2021

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

Song Luo, Kaifang Huang, Xiaoyu Zhao, Yalong Cong, John Z. H. Zhang, Lili Duan

Nanoscale

DOI

2020

相互作用熵方法在计算生物分子体系结合自由能中的发展和应用

段莉莉，黄开放，钟素素

《山东师范大学学报(自然科学版)》

2020

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

Kaifang Huang, Song Luo, Yalong Cong, Susu Zhong, John Z. H. Zhang, Lili Duan

Nanoscale

DOI

2020

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, Kaifang Huang, Song Luo, Shuheng Dong, Lili Duan

Physical Chemistry Chemical Physics

DOI

2020

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

Yalong Cong, Kaifang Huang, Yuchen Li, Susu Zhong, John Z. H. Zhang, Lili Duan

Nanoscale

DOI

2019

Study on the Amyloid Aβ42 with Accelerated Molecular Dynamics Simulations

黄开放，董淑衡，钟素素，李皓，段莉莉

Communications in Theoretical Physics

2019

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

Zhengrong Xiao, Yalong Cong, Kaifang Huang, Susu Zhong, John Z. H. Zhang, Lili Duan

Physical Chemistry Chemical Physics

DOI

2018

极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用

李宇辰，冯国强，段莉莉

《计算物理》

2018

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

Yuchen Li, Yalong Cong, Guoqiang Feng, Susu Zhong, John Z. H. Zhang, Huiyong Sun, Lili Duan

Structural Dynamics

DOI

2017

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, Lizhi Wang, Qinggang Zhang

Physical Chemistry Chemical Physics

DOI

2017

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

Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John Z. H. Zhang

Physical Chemistry Chemical Physics

DOI

2016

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

Lili Duan, Xiao Liu, John Z. H. Zhang

Journal of the American Chemical Society

DOI

2014

分子动力学和丙氨酸变异研究MDM2与抑制剂P4的结合模式

陈建中，梁志强，王伟，时术华，张少龙，段莉莉，张庆刚

《原子与分子物理学报》

2013

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

Yongxiu Li, Ya Gao, Xuqiang Zhang, Xingyu Wang, Lirong Mou, Lili Duan, Xiao Dong He, Ye Mei, John Z. H. Zhang

Journal of Molecular Modeling

DOI

2012

分子动力学模拟研究多肽Trp-cage的折叠机制

段莉莉，张庆刚

《现代化工》

2011

Protein's electronic polarization contributes significantly to its catalytic function

Yun Xiang, Lili Duan, John Z. H. Zhang

The Journal of Chemical Physics

DOI

2010

量子化学方法对生物体系的研究以及蛋白质折叠

段莉莉

《山东师范大学》

2010

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

Lili Duan, Ye Mei, Yongle Li, Qinggang Zhang, Dawei Zhang, John Z. H. Zhang

Science China Chemistry

DOI

2008

HIV蛋白酶与抑制剂的结合自由能计算

段莉莉，张庆刚

《德州学院学报》

2007

MDM2蛋白与抑制剂IMZ相互作用的研究

孟凡胜，张庆刚，段莉莉，徐博

《山东师范大学学报(自然科学版)》

2007

分子碎片共轭帽基团法研究蛋白质相互作用能

段莉莉，仝艳，孟凡胜，刘新国，时术华，张庆刚

《山东师范大学学报(自然科学版)》

会议论文

2018

在MD模拟的基础上探究凝血酶与小分子的结合机制

钟素素，李宇辰，段莉莉

《第七届全国计算原子与分子物理学术会议摘要集》

预印本

2026

Binding mechanism of the molecular glue inhibitor in overcoming the "undruggable" mutant Kirsten rat sarcoma viral oncogene homolog through conformational remodeling

Houde Liang, Xiaole Xu, Enhao Zhang, Jinxin Liu, Yihan Wang, Xinguo Liu, Song Luo, Lili Duan

SSRN Electronic Journal

DOI

段莉莉

精选作品

期刊论文

温度耦合分子动力学探测蛋白质-配体解离动力学（英文）

Unraveling the Structural Basis for Antibody Synergy against Escape-Resistant Nipah Virus Mutant

Structural Basis of SARS-CoV-2 Nsp13-Derived Peptide-Mediated NK Cell Activation

Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation

甲型流感病毒突变诱发的神经氨酸酶耐药性机制理论研究（英文）

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

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

相互作用熵方法在计算生物分子体系结合自由能中的发展和应用

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

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

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

Study on the Amyloid Aβ42 with Accelerated Molecular Dynamics Simulations

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

极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用

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

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

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

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

分子动力学和丙氨酸变异研究MDM2与抑制剂P4的结合模式

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

分子动力学模拟研究多肽Trp-cage的折叠机制

Protein's electronic polarization contributes significantly to its catalytic function

量子化学方法对生物体系的研究以及蛋白质折叠

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

HIV蛋白酶与抑制剂的结合自由能计算

MDM2蛋白与抑制剂IMZ相互作用的研究

分子碎片共轭帽基团法研究蛋白质相互作用能

会议论文

在MD模拟的基础上探究凝血酶与小分子的结合机制

预印本

Binding mechanism of the molecular glue inhibitor in overcoming the "undruggable" mutant Kirsten rat sarcoma viral oncogene homolog through conformational remodeling

研究方向