Articles

  1. Long, Pengpeng; Zhang, Lu; Huang, Bin; Chen, Quan*; Haiyan, Liu*; Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites; Nucleic Acid Research 2020, in press, doi: 10.1093/nar/gkaa1134.
  2. Sarfaraz, Sara; Muneer, Iqra; Liu, Haiyan*; Combining fragment docking with graph theory to improve ligand docking for homology model structures. J. Computer-aided Mol design 2020, 34:1237-1259. doi: 10.1007/s10822-020-00345-7.
  3. Xiong, Peng; Hu, Xiuhong; Huang, Bin; Zhang, Jiahai; Chen, Quan*; Liu, Haiyan*; Increasing the efficiency and accuracy of the ABACUS protein sequence design method; Bioinformatics, 2020, 36:136-144.
  4. Han, Mingjie; Liao, Sanhui; Xiong, Peng; Zhou, Xiaoqun; Chen, Quan*; Liu, Haiyan*; Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures; Protein Sci., 2019,28:1437-1447.
  5. Tao, Feng; Liu, Haiyan*; Molecular Dynamics Simulations Reveal Differentiated Context-Dependent Conformational Dynamics of Two Proteins of the Same Family; Journal of Physical Chemistry B 2018, 122:10686-10699. doi: 10.1021/acs.jpcb.8b08468.
  6. Chu, Huanyu; Liu, Haiyan*; TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones. Journal of Chemical Information and Modeling 2018, 58:430-442. doi: 10.1021/acs.jcim.7b00677.
  7. Xiong, Peng; Chen Quan*; Liu, Haiyan*; Computational Protein Design Under a Given Backbone Structure with the ABACUS Statistical Energy Function; Methods in Molecular Biology 2017, 1529:217-226.
  8. Tao, Rongkun; Zhao, Yuzheng; Chu, Huanyu; Wang, Aoxue; Zhu, Jiahuan; Chen, Xianjun; Zou, Yejun; Shi, Mei; Liu, Renmei; Su, Ni; Du, Jiulin; Zhou, Hai-Meng; Zhu, Linyong; Qian, Xuhong; Liu, Haiyan*; Loscalzo, Joseph; Yang, Yi*; Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism; Nature Methods 2017,14:720-728.
  9. Wang, Jichao; Zhang, Tongchuan; Liu, Ruicun; Song, Meilin; Wang, Juncheng; Hong, Jiong; Chen, Quan*; Liu, Haiyan*; Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs; Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2017, 1865:165-175.
  10. Han, Tiyun; Chen, Quan*; Liu, Haiyan*; Engineered Photoactivatable Genetic Switches Based on the Bacterium Phage T7 RNA Polymerase; ACS Synthetic Biology 2017,6:357-366.
  11. Zhou, Xiaoqun; Xiong, Peng; Wang, Meng; Ma, Rongsheng;Zhang, Jiahai; Chen, Quan*; Liu, Haiyan*; Proteins of Well-defined Structures can be designed without Backbone Readjustment by a Statistical Model; Journal of Structural Biology 2016,196:350-357.
  12. Liu, Haiyan*; Chen, Quan; Computational protein design for given backbone: Recent progresses in general method-related aspects; Current Opinions in Structural Biology 2016,39:89-95.
  13. Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen Xuetong; Wang, Weiwu*; Cai, Gang*; Structure of the intact ATM/Tel1 kinase; Nature Communications 2016,7:11655.
  14. Liu, Haiyan*; On statistical energy functions for biomolecular modeling and design; Quantitative Biology 2015, 3:157-167.
  15. Hu, Dongmei; Hu, Siyi; Wan, Wen; Xu, Man; Du, Ruikai; Zhao, Wei; Gao, Xiaolian; Liu, Jing; Liu, Haiyan*; Hong, Jiong*; Effective Optimization of Antibody Affinity by Phage Display Integrated with High-Throughput DNA Synthesis and Sequencing Technologies; PLoS One 2015, 10: e0129125.
  16. Xu, Man; Hu, Siyi; Ding, Bo; Fei,Caiyi; Wan, Wen; Hu, Dongmei; Du, Ruikai; Zhou, Xiaochuan; Hong, Jiong; Liu, Haiyan; Gao, Xiaolian*; Liu, Jing*; Design and construction of small perturbation mutagenesis libraries for antibody affinity maturation using massive microchip-synthesized oligonucleotides; Journal of Biotechnology 2015, 194:27-36.
  17. Zhang, Yinliang; Zhao, Zheng; Liu, Haiyan*; Deriving chemically essential interactions based on active site alignments and quantum chemical calculations: a case study on glycoside hydrolases; ACS Catalysis 2015, 5: 2559-2572.
  18. Xiong, Peng; Wang, Meng; Zhou, Xiaoqun; Zhang, Jiahai; Chen, Quan*; Liu, Haiyan*; Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability; Nature communications 2014, 5: 5330.
  19. Hu, Yue; Liu, Haiyan*; Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein;Journal of Physical Chemistry A 2014, 118: 9272-9279.
  20. Liu, Zexian; Wang, Yongbo; Zhou, Changhai; Xue, Yu; Zhao, wei*; Liu, Haiyan*, Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins; Biochimica Et Biophysica Acta (BBA)-Proteins and Proteomics 2014,1844: 171-180.
  21. Wan, Wen; Li, Lulu; Xu, Qianqian; Wang, Zhefan; Yao, Yuan; Wang, Rongliang; Zhang, Jia; Liu, Haiyan; Gao, Xiaolian*; Hong, Jiong*; Error removal in microchip-synthesized DNA using immobilized MutS;Nucleic Acids Research 2014, 42: e102.
  22. Hu, Hao*; Liu, Haiyan; Pitfall in Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Small Solutes in Solution; Journal of Physical Chemistry B 2013, 117: 6505-6511.
  23. Mai, Zhongxing; Liu, Haiyan*; Random Parameter Sampling of a Generic Three-Tier MAPK Cascade Model Reveals Major Factors Affecting Its Versatile Dynamics; PLoS One 2013, 8:e54441.
  24. Ma, Rui; Wang, Jichao; Hou, Zhonghuai*; Liu Haiyan*; Small-Number Effects: A Third Stable State in a Genetic Bistable Toggle Switch; Physical Review Letters 2012,109: 248107.
  25. Huang, Wei; Liu, Haiyan*; Optimized grid-based protein-protein docking as a global search tool followed by incorporating experimentally derivable restraints; Proteins-Structure Function and Bioinformatics 2012,80: 691-702.
  26. Liu, Haiyan*; Regulating and Programming Biological Systems With Modular Molecular Parts; Progress in Biochemistry and Biophysics 2012,39: 119-125.
  27. Hu, Yue; Hong, Wei; Shi, Yunyu; Liu, Haiyan*; Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages; Journal of Chemical Theory and Computation 2012(8) 3777-3792.
  28. Feng, Yan*; Wu, Jing; Cheng, Longjiu*; Liu, Haiyan; Anisotropy effect on global minimum structures of clusters: Two-center Lennard-Jones model; Journal of Chemical Physics 2011,135: 244108.
  29. Liu, Zhixiong;van Gunsteren, Wilfred F.; Liu, Haiyan*; Conformational state- specific free energy differences by one-step perturbation: protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields. J. Comput. Chem. 2011, 32: 2290-2297
  30. Zhao, Wei; Xu, Meng Xu; Liang, Zhi; Ding, Bo; Niu, Liwen; Liu, Haiyan*; Teng, Maikun*; Structure-based de novo prediction of zinc-binding sites in proteins of unknown function, Bioinformatics. 2011, 27: 1262-1268.
  31. Zhao, Liling; Liu, Zhijun; Cao, Zanxia; Liu, Haiyan; Wang, Jihua*; Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations; Computational and Theoretical Chemistry 2011, 978: 152-159.
  32. Kuntz A-P E; Liu HY; van Gunsteren WF*; Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling; J. Chem. Phys. 2011,135: 104106.
  33. Lin ZX; Liu HY; Riniker S; van Gunstenen WF*; 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; J. Chem. Theory Comput. 2011, 7: 3884–3897.
  34. Jian Zhan, Bo Ding, Rui Ma, Xiaoyu Ma, Xiaofeng Su, Yun Zhao, Ziqing Liu, Jiarui Wu, Haiyan Liu*, Develop Reusable and Combinable Designs for Transcriptional Logic Gates, Mol. Syst. Biol. 2010, 6:388.
  35. Li, Quan*; Cao, Zanxia; Liu, Haiyan; Improve the Prediction of RNA-Binding Residues Using Structural Neighbours. Protein Peptide Lett. 2010:17:287-296.
  36. Zhongxing Mai , Haiyan Liu*. Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving. J. Theor. Biol. 2009,259: 760-9
  37. Shen T, Shen W, Xiong Y, Liu H, Zheng H, Zhou H, Rui B, Liu J, Wu J, Shi Y*, Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds. J. Mass Spectrom. 2009, 44: 1066-80
  38. Zhanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu*, Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field. J Comput Chem. 2009, 30: 645-60.
  39. Quan Li, Changhai Zhou, Haiyan Liu*, Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities. Proteins. 2009, 74: 820-36.
  40. Zheng Zhao, Haiyan Liu*, A quantum mechanical/molecular mechanical study on the catalysis of the pyridoxal 5'-phosphate-dependent enzyme L-serine dehydratase. J Phys Chem B 2008, 112: 13091-100.
  41. Minghui Dong, Haiyan Liu*, Origins of the different metal preferences of E. coli peptide deformylase and Bacillus Thermoproteolyticus thermolysin: a comparative QM/MM study, J.Phys.Chem. B, 2008, 112: 10280-10290.
  42. Zanxia Cao, Haiyan Liu*; Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides; J. Chem. Phys., 2008,129: 015101.
  43. Cao Xu, Jun Wang, Haiyan Liu*, A Hamiltonian replica exchange approach and its application to the study of side chain type and neighbor effects on peptide backbone conformations, J. Chem. Theo. Comput., 2008,4: 1348-1359.
  44. Hong Yu, Xi Chen, Yuanyuan Hong, Yao Wang, Ping Xu, Shengdong Ke, Haiyan Liu, Jiankang Zhu, David J. Olive, and Cheng-Bin Xiang*, Activated Expression of an Arabidopsis HD-START Protein Confers Drought Tolerance with Improved Root System and Reduced Stomatal Density, Plant Cell, 2008, 20, 1134-1151.
  45. Jun Wang, Haiyan Liu*,A Bayesian-probability-based Method for Assigning Protein Backbone Dihedral Angles Based on Chemical Shifts and Local Sequences, J. Biomol. NMR, 2007,37:31-41
  46. Ling Tang, Haiyan Liu*, Comparative Molecular Dynamics Study of Thermophilic and Mesophilic Ribonuclease HI Enzymes. J. Biomol. Struct. Dyn., 2007,24: 379-392.
  47. Jiusheng Chen , Haoran Zheng*, Haiyan Liu, Junqing Niu, Jianping Liu ,Tie Shen , Bin Rui Yunyu Shi, Improving metabolic flux estimation via evolutionary optimization for convex solution space, Bioinformatics, 2007, 23: 1115-1123.
  48. Yuedong Yang, Haiyan Liu*; Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space; J. Comput. Chem, 2006,27: 1593-1602.
  49. Jun Wang, Yan Gu, Haiyan Liu*; Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling; J.Chem.Phys. 2006,125: 094907.
  50. Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren*, Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models, J. Comput. Chem. 2006,27: 1494-1504.
  51. Sanmei Cheng, Yuedong Yang, Wenrui Wang, Haiyan Liu*; Transition State Ensemble for the Folding of B Domain of Protein A: A Comparison of Distributed Molecular Dynamics Simulations with Experiments; J.Phys. Chem. B. 2005,109: 23645-23654.
  52. Husheng Ding,Yuedong Yang,Jihui Wu, Haiyan Liu*; Yunyu Shi*; Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data; Proteins, 2005,61:1050.
  53. G. Andres Cisneros; Haiyan Liu;Weitao Yang*; Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods; J. Chem. Phy. 2005,122:114502
  54. Haiyan Liu, Zhenyu Lu, G. Andres Cisneros, Weitao Yang*; Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions, J. Chem. Phys. 2004, 121: 697.
  55. Li Xie, Haiyan Liu*, Yang Weitao*; Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes, J. Chem. Phys., 2004, 120: 8039.
  56. Jianbin He,Zhiyong Zhang, Yunyu Shi, Haiyan Liu*; Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions, J. Chem. Phys. 2003, 119: 4005.
  57. Jiang Zhu, Qianqian Zhu, Yunyu Shi and Haiyan Liu*; How Good can we predict native contacts in proteins based on decoy structures and their energies? Proteins, 2003,52: 598.
  58. G. A. Cisnero, H. Liu, Y. Zhang and W. Yang*; Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase, J. Am. Chem. Soc., 2003, 125: 10384.
  59. Zhiyong Zhang, Yunyu Shi*, and Haiyan Liu*; Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys. J., 2003, 84: 3583.
  60. J-Y Hasegawa*, M. Ishida, H. Nakatsuji*, Zhengyu Lu, Haiyan Liu, Weitao Yang; Energetics of the electron transfer from bacteriopheophytin to ubiquinone in the photosynthetic reaction center of Rhodopseudomonas Viridis: theoretical study, J. Phys. Chem. B 2003,107: 838.
  61. Wei Gu, Tingting Wang, Jiang Zhu, Yunyu Shi, Haiyan Liu*; Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions, Biophysical Chemistry, 2003,104: 79.
  62. Jihua Wang*; Zhiyong Zhang; Haiyan Liu, Yunyu Shi*; Quasi-equilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model; Phys. Rev. E. 2003,67: 061903.
  63. Jiang Zhu, Yunyu Shi*, Haiyan Liu*; Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics; J. Phys. Chem. B 2002, 106: 4844.
  64. Li Xie, Haiyan Liu*; The Treatment of Solvation by a Generalized Born Model and a Self-Consistent Charge-Density Functional Theory-Based Tight-Binding Method; J. Comput. Chem. 2002, 23: 1404.
  65. Wei Gu, Jiang Zhu, Haiyan Liu*, Different Protonation states of the Bacillus Cereus Binuclear Zinc Metallo-lactamase active site studied by combined Quantum Mechanical and Molecular Mechanical sSimulations, J. Theore. Comput. Chem., 2002, 1: 69.
  66. Haiyan Liu, Marcus Elstner, Efthimios Kaxiras, Thomas Frauenheim, Jan Hermans*, Weitao Yang*; Quantum Mechanics Simulation of Protein Dynamics on Long Time Scale; Proteins, 2001, 44: 484.
  67. Jiang Zhu, Hao Fan, Haiyan Liu, Yunyu Shi*; Structure-based ligand design for flexible proteins: Application of new F-DycoBlock; J.Comput.Aid.Mol.Des.;2001,15: 979.
  68. Jiang Zhu, Haibo Yu, Hao Fan, Haiyan Liu, Yunyu Shi*, Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks; J.Comput.Aid.Mol.Des. 2001,15: 447.
  69. Haiyan Liu, Yingkai Zhang, Weitao Yang*; How is the active site of enolase organized to catalyze two different reaction steps? J. Am. Chem. Soc., 2000, 6560.
  70. Yingkai Zhang, Haiyan Liu; Weitao Yang*; Free energy calculation on enzyme reactions with an efficient iterative procedure to determine mininmum energy paths on a combined abinitio QM/MM poteintial energy surface, J. Chem. Phys., 2000, 112: 3483.
  71. Haiyan Liu*, Qiming Luo, Zhihong Duan, Yunyu Shi; Structure-based Ligand Design by Dynamically Assembling Molecular BuildingBlocks at Active Site, Proteins, 1999, 36: 462.
  72. Qingxiang Guo*, Haiyan Liu, XQ Ruan, XQ Zheng; YY Shi, YC Liu; Experimental and theoretical studies on the inclusion complexation of beta-cyclodextrin with phenothiazine derivatives; J. Incl.Phenom. Macro.; 1999,35: 487.
  73. Hu, Hao; Liu, Haiyan; Yunyu, Shi*; Incoporating Density Functional Potential in Classical Molecular Dynamics Simulation; Chinese Science Bulletin, 1998, 44: 286.
  74. Luo, Qiming; Liu, Haiyan*; Duan, Zhihong; Shi, Yunyu*; Explore the functional group binding sites at the active site of HIV protease using mutiple copy simulations. Acta Biophysica Sinica, 1998,14: 303.
  75. van Gunsteren, W.F.*; Liu, Haiyan; Mueller-Plathe, F.; The elucidation of enzymatic reaction mechanisms by computer simulation: Human Immunodeficiency Virus protease catalysis; J.Mol.Struct.(Theochem), 1998, 432: 9.
  76. Hu, Hao; Liu, Haiyan; Shi, Yunyu*; The Reaction Pathway of the Isomerization of D-xylose catalyzed by the Enzyme D-xylose Isomerase: A Theoretical Study; Proteins,1997,27: 545.
  77. Liu, Haiyan; Mark, A.E.; van Gunsteren, W.F*.; On Estimating the relative free energy of different molecular states with respect to a single reference state; J. Phys. Chem. 1996,100: 9485.
  78. Liu, Haiyan; Mueller-Plathe, F.; van Gunsteren, W.F.*;Combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV-protease;J. Mol. Biol. 1996,261: 454.
  79. Liu, Haiyan; Mueller-Plathe, F.; van Gunsteren, W. F.*; Moleuclar dynamics with a quantum-chemical potential: solvent effects on an SN2 reaction at nitrogen; Chem. Eur. J. 1996,2: 191.
  80. Mark. A.E*.; Xu, Yingwu; Liu, Haiyan; van Gunsteren, W.F.; Rapid non-empirical approaches for estimating relative binding free energies; Acta Biochimica Polonica; 1995, 42: 525.
  81. Liu, Haiyan; Mueller-Plathe, F.; van Gunsteren, W.F.*; A force field for dimethyl sulfoxide and physical properties of liquid dimethyl sulfoxide calculated using molecular dynamics simulations; J. Am. Chem. Soc., 1995, 117: 4363.
  82. Liu, Haiyan; Mueller-Plathe, F.; van Gunsteren, W.F.*; A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: solvent effects on the conformational equilibrium of dimeth-oxyethane; J. Chem. Phys., 1995: 102, 1722.
  83. Mueller-Plathe, F.*; Liu, Haiyan; van Gunsteren, W.F.; Conceptual hierarchies in polymer electrolyte simulations: from quantum chemistry to molecular dynamics;Computational Polymer Science, 1995,5: 89.
  84. Liu, Haiyan; Shi, Yunyu*; Combined molecular mechanical and quantum mechanical potential study of a nucleophilic reaction in solution; J. Comput. Chem., 1994, 15: 1311.
  85. Liu, Haiyan; Yunyu Shi*; Combination of Molecular Dynamics Simulation Program GROMOS With Semi-empirical Quantum Chemistry Method AM1; Chinese Science Bulletin, 1993,38: 2023.
  86. Liu, Haiyan; Shi, Yunyu*; Wang, Cunxin; Huang, Fuhua; On calculating the electrostatic energies of protein using a continum model; Acta Biophysica Sinica, 1991, 7: 483.
  87. Wang, Cunxin*; Liu, Haiyan; Shi, Yunyu; Huang, Fuhua; Calculating the relative free energy surface in configuration space using an integration method; Chem.Phys.Lett., 1991, 179: 475.
  88. Book/Chapters

  89. Haiyan Liu*; QM/MM energy functions, configuration optimizations and free energy simulations of enzyme catalysis, in Kinetics and Dynamics: from Nano to Bio-Scale, Challenges and Advances in Computational Chemistry and Physics, Eds P.Paneth and A. DybalaDefratyka, , Springer Verlag, 2010.
  90. Haiyan Liu*, Zhiyong Zhang, Jianbin He, Yunyu Shi; Using collective coordinates to guide conformational sampling in atomic simulations. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Eds Q. Cui and I. Bahar, Chapman & Hall/CRC 2006.
  91. Yingkai Zhang, Haiyan Liu, Weitao Yang*; Ab initio QM/MM and free energy calculations of enzyme reactions, in Computational Methods for Macromolecules: Challenges,Methods, Ideas - Proceedings of the 3rd International workshop on Algorithms for Macromolecullar Modelling, New York, October 13-15, 2000. Eds. Schlick, T. and Gan, H.H. Lecture Notes in Computational Science and Engineering , Springer Verlag, 2002.
  92. Zhengyu Lu, Haiyan Liu, Marcus Elstner, Weitao Yang*, Parameterization of COSMO Solvent Model for Self-Consistent charge Density-Functional Based Tight-Binding Calculations;in REVIEWS OF MODERN QUANTUM CHEMISTRY A Celebration of the Contributions of Robert G Parr, K.D. Sen Ed, World Scientific, Singapore, 2002.
  93. Mark. A. E.*; Scheafer, Heiko; Liu, Haiyan, van Gunsteren, W.F.; Estimating relative free energies from a single simulation of the initial state; in Computational Molecular Dynmiacs: Chanllenges, Mothods, Ideas; Deufhard, P.; Hermans, J.; Leimkuhler, B., Mark, A.E.; Reich, S.; Skeel R.D.; (Eds.); Springer-verlag Berlin Heidelberg, 1999, PP149-162.