刘海燕｜中国科学技术大学｜学者主页

2026

Zero-shot deep learning with multi-objective optimization improves thermostability of zearalenone hydrolase and xylanase

Fan Wu, Rongjie Wu, Linghui Chen, Quan Chen, Haiyan Liu

New Biotechnology

DOI

2026

Designing substrate-specific metalloproteases

Haiyan Liu

Vita

DOI

2025

Enhancing functional proteins through multimodal inverse folding with ABACUS-T

Yufeng Liu, Rui Wu, Xinyu Wang, Sheng Wang, Ling-Hui Chen, Fudong Li, Quan Chen, Haiyan Liu

Nature Communications

DOI

2025

Designing flexible protein structures and sampling protein conformations with a unified model using vector quantization and diffusion

Yufeng Liu, Ling-Hui Chen, Quan Chen, Haiyan Liu

National Science Review

DOI

2025

Artificial intelligence is transforming the study of proteins: Structures and beyond

Haiyan Liu, Quan Chen, Yufeng Liu

hLife

DOI

2024

De novo design of cavity-containing proteins with a backbone-centered neural network energy function

Yang Xu, Xiuhong Hu, Chenchen Wang, Yongrui Liu, Quan Chen, Haiyan Liu

Structure

DOI

2024

De novo protein design with a denoising diffusion network independent of pretrained structure prediction models

Yufeng Liu, Sheng Wang, Jixin Dong, Ling-Hui Chen, Xinyu Wang, Lei Wang, Fudong Li, Chenchen Wang, Jiahai Zhang, Yuzhu Wang, Si Wei, Quan Chen, Haiyan Liu

Nature Methods

DOI

2024

Designing de novo D-protein binders

Haiyan Liu

Cell Research

DOI

2024

Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein

Xiuhong Hu, Yang Xu, Junxi Yi, Chenchen Wang, Zhongliang Zhu, Ting Yue, Haiyan Zhang, Xinyu Wang, Fan Wu, Lin Xue, Li Bai, Haiyan Liu, Quan Chen

ACS Synthetic Biology

DOI

2023

人工智能：开启生物体系计算设计的新篇章

刘海燕

《合成生物学》

2023

Protein sequence design on given backbones with deep learning

Yufeng Liu, Haiyan Liu

Protein Engineering Design and Selection

DOI

2023

Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain

Xiuhong Hu, Yang Xu, Chenchen Wang, Yufeng Liu, Lu Zhang, Jiahai Zhang, Wenning Wang, Quan Chen, Haiyan Liu

Proceedings of the National Academy of Sciences

DOI

2023

Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function

Lu Zhang, Haiyan Liu

Journal of Computer-Aided Molecular Design

DOI

2022

A backbone-centred energy function of neural networks for protein design

Bin Huang, Yang Xu, Xiuhong Hu, Yongrui Liu, Shanhui Liao, Jiahai Zhang, Chengdong Huang, Jingjun Hong, Quan Chen, Haiyan Liu

Nature

DOI

2022

Computational protein design with data‐driven approaches: Recent developments and perspectives

Haiyan Liu, Quan Chen

Wiley Interdisciplinary Reviews Computational Molecular Science

DOI

2022

Publisher Correction: Rotamer-free protein sequence design based on deep learning and self-consistency

Yufeng Liu, Lu Zhang, Weilun Wang, Min Zhu, Chenchen Wang, Fudong Li, Jiahai Zhang, Houqiang Li, Quan Chen, Haiyan Liu

Nature Computational Science

DOI

2022

Rotamer-free protein sequence design based on deep learning and self-consistency

Yufeng Liu, Lu Zhang, Weilun Wang, Min Zhu, Chenchen Wang, Fudong Li, Jiahai Zhang, Houqiang Li, Quan Chen, Haiyan Liu

Nature Computational Science

DOI

2022

DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules

Yaoxi Chen, Quan Chen, Haiyan Liu

Journal of Chemical Information and Modeling

DOI

2021

蛋白质计算设计：方法和应用展望

操帆，陈耀晞，缪阳洋，张璐，刘海燕

《合成生物学》

2021

De novo sequence redesign of a functional Ras‐binding domain globally inverted the surface charge distribution and led to extreme thermostability

Ruicun Liu, Jichao Wang, Peng Xiong, Quan Chen, Haiyan Liu

Biotechnology and Bioengineering

DOI

2021

Computational Redesign of a PETase for Plastic Biodegradation under Ambient Condition by the GRAPE Strategy

Yinglu Cui, Yanchun Chen, Xinyue Liu, Saijun Dong, Yu’e Tian, Yuxin Qiao, Ruchira Mitra, Jing Han, Chunli Li, Xu Han, Weidong Liu, Quan Chen, Wangqing Wei, Xin Wang, Wenbin Du, Shuang‐Yan Tang, Hua Xiang, Haiyan Liu, Yong Fang Liang, Kendall N. Houk, Bian Wu

ACS Catalysis

DOI

2020

Combining fragment docking with graph theory to improve ligand docking for homology model structures

Sara Sarfaraz, Iqra Muneer, Haiyan Liu

Journal of Computer-Aided Molecular Design

DOI

2019

数据与计算驱动的蛋白质元件预测和设计

刘海燕，陈泉，龙朋朋，黄斌，许洋，陈耀晞

《生命科学》

DOI

2019

Increasing the efficiency and accuracy of the ABACUS protein sequence design method

Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen, Haiyan Liu

Bioinformatics

DOI

2019

[Computational chemistry approaches in studies on industrial enzymes].

Haiyan Liu

PubMed

DOI

2019

Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures

Ming‐Jie Han, Sanhui Liao, Peng Xiong, Xiaoqun Zhou, Quan Chen, Haiyan Liu

Protein Science

DOI

2018

细菌多元基因编辑技术研究进展及其在合成生物学中的应用

郭明璋，刘海燕，杜若曦，许文涛

《生物技术通报》

2018

Molecular Dynamics Simulations Reveal Differentiated Context-Dependent Conformational Dynamics of Two Proteins of the Same Family

Feng Tao, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2018

TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones

Huanyu Chu, Haiyan Liu

Journal of Chemical Information and Modeling

DOI

2016

Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs

Jichao Wang, Tongchuan Zhang, Ruicun Liu, Meilin Song, Juncheng Wang, Jiong Hong, Quan Chen, Haiyan Liu

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

DOI

2016

Proteins of well-defined structures can be designed without backbone readjustment by a statistical model

Xiaoqun Zhou, Peng Xiong, Meng Wang, Rongsheng Ma, Jiahai Zhang, Quan Chen, Haiyan Liu

Journal of Structural Biology

DOI

2016

Computational protein design for given backbone: recent progresses in general method-related aspects

Haiyan Liu, Quan Chen

Current Opinion in Structural Biology

DOI

2015

生物体系的多层次计算设计与合成生物学

刘海燕，黄斌

《中国科学:生命科学》

2015

On statistical energy functions for biomolecular modeling and design

Haiyan Liu

Quantitative Biology

DOI

2015

Deriving Chemically Essential Interactions Based on Active Site Alignments and Quantum Chemical Calculations: A Case Study on Glycoside Hydrolases

Yinliang Zhang, Zheng Zhao, Haiyan Liu

ACS Catalysis

DOI

2014

Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability

Peng Xiong, Meng Wang, Xiaoqun Zhou, Tongchuan Zhang, Jiahai Zhang, Quan Chen, Haiyan Liu

Nature Communications

DOI

2014

Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein

Yue Hu, Haiyan Liu

The Journal of Physical Chemistry A

DOI

2013

Pitfall in Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Small Solutes in Solution

Hao Hu, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2013

Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins

Zexian Liu, Yongbo Wang, Changhai Zhou, Yu Xue, Wei Zhao, Haiyan Liu

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

DOI

2012

用模块化分子元件调控和编程生物系统

刘海燕

《生物化学与生物物理进展》

2012

Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages

Yue Hu, Wei Hong, Yunyu Shi, Haiyan Liu

Journal of Chemical Theory and Computation

DOI

2011

面向工程化的合成生物学功能器件创建与集成初探

刘海燕

《生物产业技术》

2011

On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices

Zhixiong Lin, Haiyan Liu, Sereina Riniker, Wilfred F. van Gunsteren

Journal of Chemical Theory and Computation

DOI

2011

Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints

Wei Huang, Haiyan Liu

Proteins Structure Function and Bioinformatics

DOI

2011

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

Wei Zhao, Meng Xu, Zhi Guo Liang, Bo Ding, Liwen Niu, Haiyan Liu, Maikun Teng

Bioinformatics

DOI

2011

Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Liling Zhao, Zhijun Liu, Zanxia Cao, Haiyan Liu, Jihua Wang

Computational and Theoretical Chemistry

DOI

2011

Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling

Anna‐Pitschna E. Kunz, Haiyan Liu, Wilfred F. van Gunsteren

The Journal of Chemical Physics

DOI

2011

Conformational state‐specific free energy differences by one‐step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields

Zhixiong Lin, Wilfred F. van Gunsteren, Haiyan Liu

Journal of Computational Chemistry

DOI

2010

Using one‐step perturbation to predict the effect of changing force‐field parameters on the simulated folding equilibrium of a β‐peptide in solution

Zhixiong Lin, Haiyan Liu, Wilfred F. van Gunsteren

Journal of Computational Chemistry

DOI

2008

蛋白质结构与动力学的计算机模拟:从方法到应用

刘海燕

《中国科学技术大学学报》

2008

A Quantum Mechanical/Molecular Mechanical Study on the Catalysis of the Pyridoxal 5′-Phosphate-Dependent Enzyme l -Serine Dehydratase

Zheng Zhao, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2008

Fragment‐based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities

Quan Li, Changhai Zhou, Haiyan Liu

Proteins Structure Function and Bioinformatics

DOI

2008

Origins of the Different Metal Preferences of Escherichia coli Peptide Deformylase and Bacillus thermoproteolyticus Thermolysin: A Comparative Quantum Mechanical/Molecular Mechanical Study

Ming-Hui Dong, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2008

A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations

Chao Xu, Jun Wang, Haiyan Liu

Journal of Chemical Theory and Computation

DOI

2008

Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field

Zanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu

Journal of Computational Chemistry

DOI

2008

Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides

Zanxia Cao, Haiyan Liu

The Journal of Chemical Physics

DOI

2007

A Comparative Molecular Dynamics Study of Thermophilic and Mesophilic Ribonuclease HI Enzymes

Ling Tang, Haiyan Liu

Journal of Biomolecular Structure and Dynamics

DOI

2007

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

Wen Cai Lu, Haiyan Liu

Chinese Journal of Chemical Physics

DOI

2006

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Jun Wang, Haiyan Liu

Journal of Biomolecular NMR

DOI

2006

Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling

Jun Wang, Yan Gu, Haiyan Liu

The Journal of Chemical Physics

DOI

2006

Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space

Yuedong Yang, Haiyan Liu

Journal of Computational Chemistry

DOI

2005

Transition State Ensemble for the Folding of B Domain of Protein A: A Comparison of Distributed Molecular Dynamics Simulations with Experiments

Shanmei Cheng, Yuedong Yang, Wenrui Wang, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2005

Structural basis for SUMO‐E2 interaction revealed by a complex model using docking approach in combination with NMR data

Husheng Ding, Yuedong Yang, Jiahai Zhang, Jihui Wu, Haiyan Liu, Yunyu Shi

Proteins Structure Function and Bioinformatics

DOI

2005

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order “chain-of-replicas” methods

Gerardo Andrés Cisneros, Haiyan Liu, Zhenyu Lu, Weitao Yang

The Journal of Chemical Physics

DOI

2004

三肽和四肽构象空间的可视化方法

陈双平，郑浩然，刘海燕，王煦法

《生物物理学报》

2004

压强温度耦合作用下小蛋白去折叠过程的分子动力学模拟

王吉华，张志勇，刘海燕，施蕴渝

《生物物理学报》

2004

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions

Haiyan Liu, Zhenyu Lu, Gerardo Andrés Cisneros, Weitao Yang

The Journal of Chemical Physics

DOI

2004

Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes

Li Xie, Haiyan Liu, Weitao Yang

The Journal of Chemical Physics

DOI

2003

How well can we predict native contacts in proteins based on decoy structures and their energies?

Jiang Zhu, Qianqian Zhu, Yunyu Shi, Haiyan Liu

Proteins Structure Function and Bioinformatics

DOI

2003

Molecular Dynamics Simulations of Peptides and Proteins with Amplified Collective Motions

Zhiyong Zhang, Yunyu Shi, Haiyan Liu

Biophysical Journal

DOI

2003

Ab Initio QM/MM Study Shows There Is No General Acid in the Reaction Catalyzed by 4-Oxalocrotonate Tautomerase

Gerardo Andrés Cisneros, Haiyan Liu, Yingkai Zhang, Weitao Yang

Journal of the American Chemical Society

DOI

2003

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

Jianbin He, Zhiyong Zhang, Yunyu Shi, Haiyan Liu

The Journal of Chemical Physics

DOI

2003

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions

Wei Gu, Tingting Wang, Jiang Zhu, Yunyu Shi, Haiyan Liu

Biophysical Chemistry

DOI

2002

Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics

Jiang Zhu, Yunyu Shi, Haiyan Liu

The Journal of Physical Chemistry B

DOI

2002

The treatment of solvation by a generalized Born model and a self‐consistent charge‐density functional theory‐based tight‐binding method

Li Xie, Haiyan Liu

Journal of Computational Chemistry

DOI

2002

DIFFERENT PROTONATION STATES OF THE BACILLUS CEREUS BINUCLEAR ZINC METALLO-β-LACTAMASE ACTIVE SITE STUDIED BY COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL SIMULATIONS

Wei Gu, Jiang Zhu, Haiyan Liu

Journal of Theoretical and Computational Chemistry

DOI

2001

Quantum mechanics simulation of protein dynamics on long timescale

Haiyan Liu, Marcus Elstner, Efthimios Kaxiras, Thomas Frauenheim, Jan Hermans, Weitao Yang

Proteins Structure Function and Bioinformatics

DOI

2001

Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

Jiang Zhu, Hao Fan, Haiyan Liu, Yunyu Shi

Journal of Computer-Aided Molecular Design

DOI

2001

Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks

Jiang Zhu, Haibo B. Yu, Hao Fan, Haiyan Liu, Yunyu Shi

Journal of Computer-Aided Molecular Design

DOI

2000

How Is the Active Site of Enolase Organized To Catalyze Two Different Reaction Steps?

Haiyan Liu, Yingkai Zhang, Weitao Yang

Journal of the American Chemical Society

DOI

1999

Structure-based ligand design by dynamically assembling molecular building blocks at binding site

Haiyan Liu, Zhihong Duan, Qiming Luo, Yunyu Shi

Proteins Structure Function and Bioinformatics

DOI

1999

Incorporating density functional potential in classical molecular dynamics simulation

Hao Hu, Haiyan Liu, Yunyu Shi

Chinese Science Bulletin

DOI

1998

分子设计:用多拷贝分子动力学模拟方法搜索HIV蛋白酶活性中心的官能团结合位点

罗奇鸣，刘海燕，段志红，施蕴渝

《生物物理学报》

1991

根据连续介质模型计算蛋白质分子内静电相互作用能

刘海燕，施蕴渝，王存新，黄复华

《生物物理学报》

精选作品

期刊论文

Zero-shot deep learning with multi-objective optimization improves thermostability of zearalenone hydrolase and xylanase

Designing substrate-specific metalloproteases

Enhancing functional proteins through multimodal inverse folding with ABACUS-T

Designing flexible protein structures and sampling protein conformations with a unified model using vector quantization and diffusion

Artificial intelligence is transforming the study of proteins: Structures and beyond

De novo design of cavity-containing proteins with a backbone-centered neural network energy function

De novo protein design with a denoising diffusion network independent of pretrained structure prediction models

Designing de novo D-protein binders

Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein

人工智能：开启生物体系计算设计的新篇章

Protein sequence design on given backbones with deep learning

Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain

Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function

A backbone-centred energy function of neural networks for protein design

Computational protein design with data‐driven approaches: Recent developments and perspectives

Publisher Correction: Rotamer-free protein sequence design based on deep learning and self-consistency

Rotamer-free protein sequence design based on deep learning and self-consistency

DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules

蛋白质计算设计：方法和应用展望

De novo sequence redesign of a functional Ras‐binding domain globally inverted the surface charge distribution and led to extreme thermostability

Computational Redesign of a PETase for Plastic Biodegradation under Ambient Condition by the GRAPE Strategy

Combining fragment docking with graph theory to improve ligand docking for homology model structures

数据与计算驱动的蛋白质元件预测和设计

Increasing the efficiency and accuracy of the ABACUS protein sequence design method

[Computational chemistry approaches in studies on industrial enzymes].

Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures

细菌多元基因编辑技术研究进展及其在合成生物学中的应用

Molecular Dynamics Simulations Reveal Differentiated Context-Dependent Conformational Dynamics of Two Proteins of the Same Family

TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones

Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs

Proteins of well-defined structures can be designed without backbone readjustment by a statistical model

Computational protein design for given backbone: recent progresses in general method-related aspects

生物体系的多层次计算设计与合成生物学

On statistical energy functions for biomolecular modeling and design

Deriving Chemically Essential Interactions Based on Active Site Alignments and Quantum Chemical Calculations: A Case Study on Glycoside Hydrolases

Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability

Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein

Pitfall in Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Small Solutes in Solution

Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins

用模块化分子元件调控和编程生物系统

Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages

面向工程化的合成生物学功能器件创建与集成初探

On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices

Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling

Conformational state‐specific free energy differences by one‐step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields

Using one‐step perturbation to predict the effect of changing force‐field parameters on the simulated folding equilibrium of a β‐peptide in solution

蛋白质结构与动力学的计算机模拟:从方法到应用

A Quantum Mechanical/Molecular Mechanical Study on the Catalysis of the Pyridoxal 5′-Phosphate-Dependent Enzyme l -Serine Dehydratase

Fragment‐based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities

Origins of the Different Metal Preferences of Escherichia coli Peptide Deformylase and Bacillus thermoproteolyticus Thermolysin: A Comparative Quantum Mechanical/Molecular Mechanical Study

A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations

Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field

Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides

A Comparative Molecular Dynamics Study of Thermophilic and Mesophilic Ribonuclease HI Enzymes

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling

Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space

Transition State Ensemble for the Folding of B Domain of Protein A: A Comparison of Distributed Molecular Dynamics Simulations with Experiments

Structural basis for SUMO‐E2 interaction revealed by a complex model using docking approach in combination with NMR data

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order “chain-of-replicas” methods

三肽和四肽构象空间的可视化方法

压强温度耦合作用下小蛋白去折叠过程的分子动力学模拟

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions

Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes

How well can we predict native contacts in proteins based on decoy structures and their energies?

Molecular Dynamics Simulations of Peptides and Proteins with Amplified Collective Motions

Ab Initio QM/MM Study Shows There Is No General Acid in the Reaction Catalyzed by 4-Oxalocrotonate Tautomerase

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions

Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics

The treatment of solvation by a generalized Born model and a self‐consistent charge‐density functional theory‐based tight‐binding method

DIFFERENT PROTONATION STATES OF THE BACILLUS CEREUS BINUCLEAR ZINC METALLO-β-LACTAMASE ACTIVE SITE STUDIED BY COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL SIMULATIONS

Quantum mechanics simulation of protein dynamics on long timescale

Structure-based ligand design for flexible proteins: Application of new F-DycoBlock