Haiyan Liu

发表

Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface

Weitao Yang, Yingkai Zhang, Haiyan Liu, 2000 .

Molecular dynamics simulations of peptides and proteins with amplified collective motions.

Haiyan Liu, Yunyu Shi, Zhiyong Zhang, 2003, Biophysical journal.

Improve the prediction of RNA-binding residues using structural neighbours.

Zanxia Cao, Haiyan Liu, Z. Cao, 2010, Protein and peptide letters.

Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions

Weitao Yang, Yingkai Zhang, Haiyan Liu, 2002 .

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

Qianqian Zhu, Jiang Zhu, Haiyan Liu, 2003, Proteins.

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

Zexian Liu, Yongbo Wang, Yu Xue, 2014, Biochimica et Biophysica Acta.

Error removal in microchip-synthesized DNA using immobilized MutS

Yuan Yao, Xiaolian Gao, Jiong Hong, 2014, Nucleic acids research.

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

Haiyan Liu, Haiyan Liu, Quan Li, 2009, Proteins.

Case study on temperature-accelerated molecular dynamics simulation of ligand dissociation: inducer dissociation from the Lac repressor protein.

Haiyan Liu, Yue Hu, 2014, The journal of physical chemistry. A.

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Haiyan Liu, Hao Hu, 2013, The journal of physical chemistry. B.

QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis

Haiyan Liu, 2010 .

The elucidation of enzymatic reaction mechanisms by computer simulation: Human immunodeficiency virus protease catalysis

W. V. Gunsteren, F. Müller-Plathe, Haiyan Liu, 1998 .

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

Haiyan Liu, Jun Wang, 2006, Journal of biomolecular NMR.

Develop reusable and combinable designs for transcriptional logic gates

Jian Zhan, J. Zhan, Haiyan Liu, 2010, Molecular systems biology.

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

Jun Wang, Chao Xu, Chao Xu, 2008, Journal of chemical theory and computation.

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

Weitao Yang, Zhenyu Lu, Weitao Yang, 2004, The Journal of chemical physics.

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase.

Weitao Yang, Yingkai Zhang, Haiyan Liu, 2003, Journal of the American Chemical Society.

Putative global minimum structures of Morse clusters as a function of the range of the potential: 161 < or = N < or = 240.

Yan Feng, Longjiu Cheng, Longjiu Cheng, 2009, The journal of physical chemistry. A.

Anisotropy effect on global minimum structures of clusters: two-center Lennard-Jones model.

Longjiu Cheng, Haiyan Liu, Yan Feng, 2011, The Journal of chemical physics.

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

Jiang Zhu, Haiyan Liu, W. Gu, 2002 .

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

Haiyan Liu, Wei Zhao, Bo Ding, 2011, Bioinform..

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

Jihua Wang, Haiyan Liu, Z. Cao, 2011 .

Energetics of the Electron Transfer from Bacteriopheophytin to Ubiquinone in the Photosynthetic Reaction Center of Rhodopseudomonas Viridis: Theoretical Study

Weitao Yang, H. Nakatsuji, Haiyan Liu, 2003 .

The reaction pathway of the isomerization of d‐xylose catalyzed by the enzyme d‐xylose isomerase: A theoretical study

Haiyan Liu, Yunyu Shi, Hao Hu, 1997, Proteins.

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

Haiyan Liu, Yinliang Zhang, Zheng Zhao, 2015 .

Molecular dynamics simulations of liquid methanol and methanol–water mixtures with polarizable models

Haiyan Liu, Wilfred F. van Gunsteren, Daan P. Geerke, 2006, J. Comput. Chem..

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

Haiyan Liu, Wilfred F. van Gunsteren, Zhixiong Lin, 2010, J. Comput. Chem..

Molecular Dynamics Simulations of Peptides and Proteins with Ampliﬁed Collective Motions

Haiyan Liu, Zhiyong Zhang, Yunyu Shi, 2003 .

Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

Haiyan Liu, Minghui Dong, 2008, The journal of physical chemistry. B.

Improving metabolic flux estimation via evolutionary optimization for convex solution space

Haiyan Liu, Jiusheng Chen, Yunyu Shi, 2007, Bioinform..

Random Parameter Sampling of a Generic Three-Tier MAPK Cascade Model Reveals Major Factors Affecting Its Versatile Dynamics

Zhong Mai, Haiyan Liu, Haiyan Liu, 2013, PloS one.

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

L. Tang, Haiyan Liu, Ling Tang, 2007, Journal of biomolecular structure & dynamics.

Effective Optimization of Antibody Affinity by Phage Display Integrated with High-Throughput DNA Synthesis and Sequencing Technologies

Xiaolian Gao, Jing Liu, Jiong Hong, 2015, PloS one.

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

Haiyan Liu, Sara Sarfaraz, Iqra Muneer, 2020, Journal of Computer-Aided Molecular Design.

Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving.

Zhong Mai, Haiyan Liu, Haiyan Liu, 2009, Journal of theoretical biology.

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

Haiyan Liu, Zhixiong Lin, Jun Wang, 2009, J. Comput. Chem..

Combining statistical and neural network approaches to derive energy functions for completely flexible protein backbone design

Yang Xu, Haiyan Liu, Bin Huang, 2019, bioRxiv.

A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress

Haiyan Liu, Hong Zhou, Jiusheng Chen, 2010, BMC Systems Biology.

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

Yuedong Yang, Jiahai Zhang, Yuedong Yang, 2005, Proteins.

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, 2003, Biophysical chemistry.

Design and construction of small perturbation mutagenesis libraries for antibody affinity maturation using massive microchip-synthesized oligonucleotides.

Xiaolian Gao, Jiong Hong, Wen Wan, 2015, Journal of biotechnology.

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

Jiang Zhu, Haiyan Liu, Haiyan Liu, 2002 .

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

Haiyan Liu, F. Tao, Feng Tao, 2018, The journal of physical chemistry. B.

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

Haiyan Liu, Yunyu Shi, Zhiyong Zhang, 2003 .

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

Weitao Yang, Yingkai Zhang, Haiyan Liu, 2000 .

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

Weitao Yang, Zhenyu Lu, G Andrés Cisneros, 2005, The Journal of chemical physics.

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

Li Xie, Weitao Yang, Weitao Yang, 2004, The Journal of chemical physics.

Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State

Alan E. Mark, W. F. van Gunsteren, A. Mark, 1996 .

Incorporating density functional potential in classical molecular dynamics simulation

Haiyan Liu, Yunyu Shi, Hao Hu, 1999 .

Binding model of human coactosin-like protein with filament actin revealed by mutagenesis.

Wei Huang, Haiyan Liu, Jihui Wu, 2006, Biochimica et biophysica acta.

[Computational chemistry approaches in studies on industrial enzymes].

Haiyan Liu, Haiyan Liu, 2019, Sheng wu gong cheng xue bao = Chinese journal of biotechnology.

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

Jun Wang, Haiyan Liu, Haiyan Liu, 2006, The Journal of chemical physics.

A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation

Wilfred F. van Gunsteren, W. V. Gunsteren, Haiyan Liu, 1995 .

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

Haiyan Liu, Jiang Zhu, Hao Fan, 2001, J. Comput. Aided Mol. Des..

Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds.

Hong Zhou, Weiqun Shen, Tie Shen, 2009, Journal of mass spectrometry : JMS.

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

Haiyan Liu, Yuedong Yang, Yuedong Yang, 2006, J. Comput. Chem..

Molecular Dynamics with a Quantum‐Chemical Potential: Solvent Effects on an SN2 Reaction at Nitrogen

Wilfred F. van Gunsteren, Florian Müller-Plathe, W. V. Gunsteren, 1996 .

Quantum mechanics simulation of protein dynamics on long timescale

M Elstner, E. Kaxiras, J. Hermans, 2001, Proteins.

Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution

Haiyan Liu, Yunyu Shi, Haiyan Liu, 1994, J. Comput. Chem..

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

Haiyan Liu, Wilfred F. van Gunsteren, Zhixiong Lin, 2011, J. Comput. Chem..

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

Haiyan Liu, Li Xie, Haiyan Liu, 2002, J. Comput. Chem..

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.

Wilfred F van Gunsteren, Sereina Riniker, Zhixiong Lin, 2011, Journal of chemical theory and computation.

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

Haiyan Liu, Zanxia Cao, 2008, The Journal of chemical physics.

Estimating Relative Free Energies from a Single Simulation of the Initial State

Alan E. Mark, Haiyan Liu, Heiko Schäfer, 1999, Computational Molecular Dynamics.

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

Haiyan Liu, Haibo Yu, Jiang Zhu, 2001, J. Comput. Aided Mol. Des..

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

Wilfred F van Gunsteren, Anna-Pitschna E. Kunz, W. V. van Gunsteren, 2011, The Journal of chemical physics.

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

W. V. Gunsteren, Haiyan Liu, Zhixiong Lin, 2011, J. Comput. Chem..