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Journal Papers/Book Chapters

[23] Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization
Yang Yang, Haibo Yu, Darrin York, Qiang Cui, Marcus Elstner
submitted to Journal of Chemical Theory and Computation, 2008

[22] Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain
Haibo Yu, Yang Yang, Liang Ma, Qiang Cui
in Energy Flows in Proteins, 2008 Eds. David M. Leitner and John E. Straub, CRC Press

[21] Extensive conformational transitions are required to turn on ATP hydrolysis in myosin
Yang Yang, Haibo Yu, Qiang Cui
J. Mol. Biol. 381(5), 1407-1420, 2008

[20] Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation
Zhenyu Li, Haibo Yu, Wei Zhuang, Shaul Mukamel
Chem. Phys. Lett. 452(1-3), 78-83, 2008

[19] The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding
Haibo Yu, Qiang Cui
J. Chem. Phys. 127(23), 234504, 2007

[18] Extension of the Self-Consistent-Charge Density-Functional Tight-Bin ding (SCC-DFTB) method: third order expansion of the DFT total energy and introduction of a modified effective Coulomb interaction
Yang Yang, Haibo Yu, Darrin York, Qiang Cui, Marcus Elstner
J. Phys. Chem. A. 111(42), 10861-10873, 2007

[17] Molecular dynamics simulation of human interleukin-4: Comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability
Moritz Winger, Haibo Yu, Christina Redfield, Wilfred F. van Gunsteren
Mol. Simul. 33(14), 1143-1154 2007

[16] Mechanochemical coupling in myosin motor domain: II. Analysis of critical residues
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
PLoS Comput. Biol. 3(2), 214-230, 2007

[15] Mechanochemical coupling in myosin motor domain: I. Insights from equilibrium active-site simulations
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
PLoS Comput. Biol. 3(2), 199-213, 2007

[14] "Proton holes" in long-range proton transfers in solution and enzymes
Demian Riccardi, Peter Konig, Xavier Prat-Resina, Haibo Yu, Marcus Elstner, Thomas Frauenheim, Qiang Cui
J. Am. Chem. Soc. 128(50), 16302-16311, 2006

[13] Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins
Haibo Yu, Andreas Kohl, H. Kaspar Binz, Andreas Plueckthun, Markus G. Gruetter, Wilfred F. van Gunsteren
Proteins. 65(2), 285-295, 2006

[12] Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models
Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren
J. Comput. Chem. 27(13), 1494-1504, 2006

[11] Biomolecular modelling: goals, problems, perspectives
Wilfred F. van Gunsteren, Dirk Bakowies, Riccardo Baron, Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan P. Geerke, Alice Glaettli, Philippe Huenenberger, Mika A. Kastenholz, Chris Oostenbrink, Merijn Schenk, Daniel Trzesniak, Nico F. A. van der Vegt, Haibo Yu
Angew. Chem. Int. Ed. 45(25), 4064-4092, 2006 Angew. Chem. 118(25), 4168-4198, 2006

[10] Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes
Demian Riccardi, Partricia Schaefer, Yang Yang, Haibo Yu, Nilanjan Ghosh, Xavier Prat-Resina, Peter Koenig, Guohui Li, Dingguo Xu, Hua Guo, Marcus Elstner, Qiang Cui
J. Phys. Chem. B. 110(13), 6458-6469, 2006

[9] Accounting for polarization in molecular simulation
Haibo Yu, Wilfred F. van Gunsteren
Comput. Phys. Comm. 172(2), 69-85, 2005

[8] Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice
Haibo Yu, Wilfred F. van Gunsteren
J. Chem. Phys. 121(19), 9549-9564, 2004

[7] Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study
Haibo Yu, Manfred Amann, Tomas Hansson, Jutta Koehler, Guenter Wich, Wilfred F. van Gunsteren
Carbohydr. Res. 339(10), 1697-1709, 2004

[6] Comparison of properties of Aib-rich peptides in crystal and solution: A molecular dynamics study
Haibo Yu, Maaike Ramseier, Roland Buergi, Wilfred F. van Gunsteren
ChemPhysChem 5(5), 633-641, 2004

[5] On the transferability of the SPC/L water model to biomolecular simulation
Alice Glaettli, Chris Oostenbrink, Xavier Daura, Daan P. Geerke, Haibo Yu, Wilfred F. van Gunsteren
Brazil. J. Phys. 34(1), 116-125, 2004

[4] Molecular dynamics simulations of peptides containing an unnatural amino acid: folding, dimerization and protein binding
Haibo Yu, Xavier Daura, Wilfred F. van Gunsteren
Proteins. 54(1), 116-127, 2003

[3] Development of a simple, self-consistent polarizable model for liquid water
Haibo Yu, Tomas Hansson, Wilfred F. van Gunsteren
J. Chem. Phys. 118(1), 221-234, 2003

[2] Molecular Dynamics Simulation of Biomolecular Systems
Wilfred F. van Gunsteren, Dirk Bakowies, Roland Buergi, Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Alice Glaettli, Tomas Hansson, Chris Oostenbrink, Christine Peter, Jed Pitera, Lukas Schuler, Thereza A. Soares, Haibo Yu
CHIMIA 55(10), 856-860, 2001

[1] Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks
Jiang Zhu, Haibo Yu, Hao Fan, Haiyan Liu, Yunyu Shi
J. Comp. Aid. Mol. Des. 15(5), 447-463, 2001

Thesis and Dissertation

PhD Dissertation
Biomolecular simulation: inclusion of polarizability, prediction of conformational stability, and analysis of peptide folding and association (ISBN 3-8322-3452-7) (in English)
Dr. sc. nat. Diss. ETH No. 15670, Aug 2004, accepted on the recommendation of Prof. Dr. Wilfred F. van Gunsteren, examiner, and Prof. Dr. Herman J. C. Berendsen, Prof. Dr. Philippe H. Huenenberger, co-examiners

Bachelor Thesis
Molecular dynamics simulation of MoPrP (121-231) unfolding at low pH (in Chinese)
B. Sc. in Biological Sciences, USTC, Hefei, July 2000, supervisor: Prof. Yunyu Shi