Overview

We are interested in developing and applying computational tools for the study of structure, dynamics and interaction of biomolecules. One current focus is to develop efficient and accurate methods to simulate conformation equlibria in solution, and to apply such methods in force field improvements as well as in functional studies. Another focus is to improve protein design, including statistical energy functions, negative design and modular design.

To test and/or apply these tools, we collaborate with experimentalists (protein dynamics and conformational equilibria), or carry out experiments ourselves (protein sequence design) . For example, we are especially interested in designing highly focused sequence libraries for the efficient screening of new and specific molecular interactions. We are also attempting to integrate such designed/screened interactions with other molecular modules to create artificial signal-processing proteins that can be utilized in synthetic biological systems.

 

Our Research

Molecular dynamics simulation

Protein design

Synthetic biology

Haiyan Liu

Professor, School of Life Sciences
University of Science & Technology of China

Tel: 86-551-3607450
Fax: 86-551-3607451
E-mail: hyliu@ustc.edu.cn

Personal Profile

Haiyan Liu was born in Sichuan Province, China. He received his BS degree in Biology in 1990 and PhD degree in Biochemistry and Molecular Biology in 1996, both from USTC. Between 1993 and 1995 he was a visiting graduate student in Laboratory of Physical Chemistry of ETH, Zurich (Switzerland). From 1998 to 2000 he was post-doctoral research associate at Department of Chemistry, Duke University (USA) and Department of Biochemistry and Biophysics UNC-Chapel Hill (USA). Since 2001, he has been a professor of computational biology at School of Life Sciences, USTC.

Research Interests

We are interested in developing and applying comutational tools for the study of structure, dynamics and interaction of biomolecules. One current focus is to develop efficient and accurate methods to simulate conformation equlibria in solution, and to apply such methods in force field improvements as well as in functional studies. Another focus is to improve protein design, including statistical energy functions, negative design and modular design.

To test and/or apply these tools, we collorborate with experimentalists (protein dynamics and conformational equilibria), or carry out experiments ourselves (protein sequence design) . For example, we are especially interested in designing highly focused sequence libraries for the efficient screening of new and specific molecular interactions. We are also attempting to integrate such designed/screened interactions with other molecular modules to create artificial signal-processing proteins that can be utilized in synthetic biological systems.

Selected Publications

1. 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, in press.

2. 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.

3. 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.

4. 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-Proteins and Proteomics 2014,1844: 171-180.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. Liu, Haiyan*; Regulating and Programming Biological Systems With Modular Molecular Parts; Progress in Biochemistry and Biophysics 2012,39: 119-125.

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Quan Chen

Associate Professor, School of Life Sciences
University of Science & Technology of China

Tel: 86-551-3607450
Fax: 86-551-3600607
E-mail: chenquan@ustc.edu.cn

Personal Profile

Dr. Quan Chen obtained her Ph.D. in Biochemistry and Molecular biology from University of Science and Technology of China in 2007. Before starting her position at USTC, Quan conducted a two-year postdoctoral fellowship in Mayo Clinic Arizona focusing on structure and function studies of G-protein coupled receptors, and was a research associate at University of Southern California working on mRNA display based Zinc finger selection.

Research Interests

We are interested in the design of Artificial Transcription Factors and probing their applications in synthetic biology. Currently, we are focusing on reprogramming E.coli phenotype by developing zinc-finger based artificial transcription factors. We are also focusing on elucidate phenotype-related gene and metabolic network.

We are also attempting to design new molecular tools/switches for performing information processing and control biological functions in living systems and apply these tools to programming and probing biological systems. We are applying these technologies to address key challenges in synthetic biology including next generation bio-energy, biosynthesis as well as environmental protections.

Selected Publications

1. Miller, L.J., Chen, Q., Lam, P.C., Pinon, D.I., Sexton, P.M., Abagyan, R. and Dong, M.Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. Journal of Biological Chemistry, 2011, 286:15895-15907

2. Chen, Q., Pinon, D.I., Miller, L.J., and Dong, M. Spatial approximations between residues 6 and 12 in the amino-terminal region of glucagon-Like peptide 1 and its receptor. a region critical for biological activity. Journal of Biological Chemistry, 2010, 285: 24508-24518

3. Chen, Q., Miller, L.J., and Dong, M. Role of N-linked glycosylation in biosynthesis, trafficking, and function of the human glucagon-like peptide 1 receptor. Am. J. Physiol. Endocrinol. Metab. 2010, 299(1): E62-8

4. Chen, Q., Pinon, D.I., Miller, L.J., and Dong, M. Molecular basis of glucagon-like peptide 1 docking to its intact receptor studied with carboxyl-terminal photolabile probes. Journal of Biological Chemistry, 2009, 284: 34135-34144

5. Chen, Q., Niu, X., Xu, Y., Wu, J., and Shi, Y. Solution Structure and Backbone Dynamics of AF-6 PDZ domain/Bcr Peptide Complex. Protein Science, 2007, 16: 1053 - 1062

6. Niu, X., Chen, Q., Zhang, J., Shen, W., Shi, Y., and Wu, J. Interesting structural and dynamical behaviors exhibited by the AF-6 PDZ domain upon Bcr peptide binding. Biochemistry, 2007, 46(51):15042-15053

7. Ding, H., Xu, Y., Chen, Q., Dai, H., Tang, Y., Wu, J., and Shi, Y. Solution structure of human SUMO-3 C47S and its binding surface for Ubc9. Biochemistry, 2005, 44(8): 2790-2799

8. Zhang, X., Zhang, J., Li, X., Xu, J., Huang, H., Chen, Q., Wu, J., and Shi, Y. Compact molten globule-like state of hUBF HMG Box1 at extremely low pH. Biochimica et Biophysica Acta, 2005, 1748: 66?3

9. Chen, Q. and Shi, Y. Progress in SUMO modification research. Chinese Bulletin of Life Sciences, 2004, 16: 1-6

10. Xiao, Y., Chen, Q., Hang, J., Shi, Y., Wu, J., Hong, Y. and Wang, Y. Selective induction, purification and characterization of a laccase isozyme from the basidiomycete Trametes sp. AH28-2. Mycologia, 2004, 96(1):26-35

 

Zhe Zhang

Administrative Assistant

Email:cblab@ustc.edu.cn
Education background: B.S. in International Economics and Trade, Anhui University of Technology
Joined the lab: 2012

 

Graduate students

  • Xiong Peng

    Peng Xiong

    Email:xiongxp@mail.ustc.edu.cn
    Education background: Biology Science in USTC
    Research interest: develop statistal potential for protein design
    Joined the lab:2007

  • Yinliang Zhang

    Yinliang Zhang

    Email:zylzhang@mail.ustc.edu.cn
    Education background: B.S. in Information Security, Tongji University
    Research interest: Structural Bioinformatics to detect sequence-structure-function relationships
    Joined the lab:2008

  • Jichao Wang

    Jichao Wang

    Email:jichaow@mail.ustc.edu.cn
    Education background: B.S. in Biotechnology, AHU
    Research interest: synthetic biology (Develop transcriptional logic gates using lacI; E.coli Communication and Differentiation), protein design and experimental analysis
    Joined the lab:2009

  • Dongmei Hu

    Dongmei Hu

    Email:hud@mail.ustc.edu.cn
    Education background: B.S. in Biology Science, Central China Normal University
    Research interest: Antibody affinity maturation by phage display; Phage assisted continuous evolution.
    Joined the lab:2012

  • Yue Hu

    Yue Hu

    Email:huyue@mail.ustc.edu.cn
    Education background: B.S. in Qufu Normal University
    Research interest: Molecular dynamics simulation
    Joined the lab:2010

  • Huanyu Chu

    Huanyu Chu

    Email:huanyu@mail.ustc.edu.cn
    Education background: B.S. in Biological Science, USTC
    Research interest: MD simulation
    Joined the lab:2010

  • Xiaoqun Zhou

    Xiaoqun Zhou

    Email:qun@mail.ustc.edu.cn
    Education background: Biological sciences in Anhui Normal University
    Research interest: Biosynthesis
    Joined the lab:2011

  • Meng Wang

    Meng Wang

    Email:wmasj@mail.ustc.edu.cn
    Education background: Biological sciences in Anhui Normal University
    Research interest: Biosynthesis
    Joined the lab:2011

  • Tiyun Han

    Tiyun Han

    Email:hantiyun@sina.cn
    Education background: Biology Science in Northeastern University
    Research interest: Boichemistry and molecular biology
    Joined the lab:2012

  • Huan Wang

    Huan Wang

    Email:whustc01@mail.ustc.edu.cn
    Education background: B.S. in biology, NJAU
    Research interest: Synthetic biology
    Joined the lab:2012

  • Tongchuan Zhang

    Tongchuan Zhang

    Email:ztc08a@mail.ustc.edu.cn
    Education background: BS in Systems Biology, USTC
    Research interest: Protein Design & tructure prediction
    Joined the lab:2011

  • Ruicun Liu

    Ruicun Liu

    Email: lruicun@mail.ustc.edu.cn
    Education background: Tianjin University
    Research interest: Synthetic biology
    Joined the lab: 2013

  • Xuexuan Zheng

    Xuexuan Zheng

    Email:zhxx@mail.ustc.edu.cn
    Education background: Biology Science in USTC
    Research interest: PACE & evolution of protein-protein interaction
    Joined the lab:2013

  • Minjie Han

    Xuexuan Zheng

    Minjie Han

    Email:HanMJ@mail.ustc.edu.cn
    Education background: biological sciences in Anhui Normal University
    Research interest: biosynthesis
    Joined the lab:2014

  • Bin Huang

    Bin Huang

    Email: hb080@mail.ustc.edu.cn
    Education background: B.S. in Biology Engineering, HIT
    Research interest: Computational design of Protein-Protein interaction
    Joined the lab: 2014

 

Undergraduate student

  • Yunyi Zhu

    Yunyi Zhu

    Email: zhuyz@mail.ustc.edu.cn
    Education background: Systems Biology in USTC
    Research interest: Molecular dynamic simulation
    Joined the lab:2011

 

Visiting Scholars

  • Haiyan Li

    Haiyan Li

    Email:tianwaifeixian78@163.com
    Education background: Key Lab of Biophysics in Universities of Shandong (Dezhou University)
    Research interest: complex network ; molecular dynamics


 

Former Members

  • Wei Zhao

    Wei Zhao,Ph.d

    Postdoctoral Fellow

    Email:zhaowei@ustc.edu.cn
    Education background: PhD in Structural Biology, USTC
    Research interest: Computational structural biology; such as computational design of antibody-affinity improvement beyond in vivo maturation
    Joined the lab 2008


  • Zhixiong Lin

    Zhixiong Lin,Ph.d

    Graduate

    Email:linzx009@mail.ustc.edu.cn
    Education background: B.S. Biology, USTC
    Research interest: Using one-step perturbation to calculate conformationa-state specific free energies: a method to fast predict conformational equilibrium of biomolecules using molecular dynamic simulations.
    Joined the lab 2006

  • Meilin Song

    Meilin Song

    Graduate

    Email:smeilin@mail.ustc.edu.cn
    Education background: B.S. in Pharmacy, Shanghai Jiao Tong University; M.S. in Bioinformatics, USTC
    Research interest: TIM barrel scaffold design, Protein evolution, Data mining .
    Joined the lab 2006

  • Dudu Tong

    Dudu Tong

    Undergraduate

    Email: tongdudu@mail.ustc.edu.cn
    Education background: BS in Systems Biology, USTC
    Research interest: Protein Structure Prediction & Protein Design
    Research project: Iterative Design of TIM Hybrid Protein Based on Rosetta
    Joined the lab:2009

  • Wei Hong

    Wei Hong

    Graduate

    Email:hongwei2@mail.ustc.edu.cn
    Education background: B.S. in Biological Engineering, Northeastern University
    Research interest: molecular dynamics simulation of glycoside hydrolase
    Joined the lab:2010

  • Damaris Niggli

    Damaris Niggli

    Visiting Scholar

    Email:aniwe03@hotmail.com
    Education background: B.S. in chemistry, Swiss Federal Institute of Technology Zurich, Switzerland
    Research interest: molecular dynamics to study one step perturbation in ligand binding affinity


  • Maxime Richard

    Maxime Richard

    Visiting Scholar

    Email:maximerchrd@hotmail.com
    Education background: B.S. in chemistry, Swiss Federal Institute of Technology Zurich, Switzerland
    Research interest: molecular dynamics by enhanced sampling methods


  • Xinguang Yang

    Xinguang Yang

    Administrative Assistant

    Education background: B.S. in School of Business, Hohai University; M.S. in School of Management, USTC
    Joined the lab: 2010


  • Caiyi Fei

    Caiyi Fei

    Graduate

    Email:feicaiyi@mail.ustc.edu.cn
    Education background: B.S. in Thermodynamics, NJUST
    Research interest: Antibody library development, ANM application
    Joined the lab:2007

  • Zexian Liu

    Zexian Liu

    Graduate

    Email:lzx@mail.ustc.edu.cn
    Education background: B.S. in Life Science, USTC
    Research interest: Molecular dynamics simulation of biomacromolecular complexes
    Joined the lab:2010

 

Publications

1. Zhang, Yingliang; 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, in press.

2. 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.

3. 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.

4. 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-Proteins and Proteomics 2014,1844: 171-180.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. Liu, Haiyan*; Regulating and Programming Biological Systems With Modular Molecular Parts; Progress in Biochemistry and Biophysics 2012,39: 119-125.

11. 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.

12. 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.

13. Lin, 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

14. Zhao, Wei; Xu, Meng; 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.

15. 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.

16. 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.

17. 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.

18. Zhan, Jian; Ding, Bo; Ma, Rui; Ma, Xiaoyu; Su, Xiaofeng; Zhao, Yun; Liu, Ziqing; Wu, Jiarui; Liu, Haiyan*; Develop Reusable and Combinable Designs for Transcriptional Logic Gates; Mol. Syst. Biol. 2010, 6:388.

19. Li, Quan*; Cao, Zanxia; Liu, Haiyan; Improve the Prediction of RNA-Binding Residues Using Structural Neighbours. Protein & Peptide Letters; 2010:17:287-296.

20. Mai, Zhongxing; Liu, Haiyan*. Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving. J Theor Biol. 2009,259: 760-9

21. 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

22. 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.

23. 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.

24. 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.

25. 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.

26. 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.

27. 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. Theory Comput., 2008,4: 1348-1359.

28. 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.

29. 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

30. Ling Tang, Haiyan Liu*, Comparative Molecular Dynamics Study of Thermophilic and Mesophilic Ribonuclease HI Enzymes. J. Biomol. Struct. Dyn., 2007,24: 379-392.

31. 6. 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.

32. 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.

33. Jun Wang, Yan Gu, Haiyan Liu*; Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling; J.Chem.Phys. 2006,125: 094907.

34. 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.

35. 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.

36. 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.

37. 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

38. 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.

39. 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.

40. 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.

41. 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.

42. 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.

43. Zhiyong Zhang, Yunyu Shi*, and Haiyan Liu*; Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys. J., 2003, 84: 3583.

44. 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.

45. 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.

46. 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.

47. 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.

48. 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.

49. 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.

50. 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.

51. 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.

52. 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.

53. 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.

54. 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.

55. Haiyan Liu*, Qiming Luo, Zhihong Duan, Yunyu Shi; Structure-based Ligand Design by Dynamically Assembling Molecular BuildingBlocks at Active Site, Proteins, 1999, 36: 462.

56. 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.

57. Hu, Hao; Liu, Haiyan; Yunyu, Shi*; Incoporating Density Functional Potential in Classical Molecular Dynamics Simulation; Chinese Science Bulletin, 1998, 44: 286.

58. 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.

59. 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.

60. 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.

61. 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.

62. 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.

63. 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.

64. 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.

65. 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.

66. 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.

67. 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.

68. Liu, Haiyan; Shi, Yunyu*; Combined molecular mechanical and quantum mechanical potential study of a nucleophilic reaction in solution; J. Comput. Chem., 1994, 15: 1311.

69. Liu, Haiyan; Yunyu Shi*; Combination of Molecular Dynamics Simulation Program GROMOS With Semi-empirical Quantum Chemistry Method AM1; Chinese Science Bulletin, 1993,38: 2023.

70. 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.

71. 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.

Book/Chapers

72. 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.

73. 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.

74. 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.

75. 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.

76. 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.

ABACUS: Protein Sequence Design


ABACUS is a program for designing amino acid sequence to fold into target tertiary structure.

Target PDB structure
Copy and paste your structure file here Sample input

NOTE: Residues lack any of the backbone atom (N, CA, C, O) will be ignored. Non standard amino acid except selenomethionine (MSE) will be ignored. Residue index should be integer.


Specify amino acid choices for each position (Optional, Sample input )


Output sequence number (maximum 100):

Job Name: (Optional, your given name to this protein)

Email: (Mandatory, where results will be sent to)

Reference:

  • Xiong P, Wang M, Zhou X, et al. Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability[J]. Nature communications, 2014, 5: 5330.
  • Xiong P, Chen Q, Liu H. Computational protein design under a given backbone structure with the ABACUS statistical energy function[M]//Computational Protein Design. Humana Press, New York, NY, 2017: 217-226.

ABACUS: Predict dTM in Single Site Mutation of Protein


Target PDB structure
Copy and paste your structure file here Sample input


Specify mutation (Sample input)

Job Name: (Optional, your given name to this protein)

Email:

Reference:

  • Xiong P, Wang M, Zhou X, et al. Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability[J]. Nature communications, 2014, 5: 5330.
  • Xiong P, Chen Q, Liu H. Computational protein design under a given backbone structure with the ABACUS statistical energy function[M]//Computational Protein Design. Humana Press, New York, NY, 2017: 217-226.