Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks. - Jiang Zhu; Haibo Yu 003; Hao Fan; Haiyan Liu; Yunyu Shi (J. Comput. Aided Mol. Des., 2001)

Accounting for polarization in molecular simulation. - Haibo Yu 003; Wilfred F. van Gunsteren (Comput. Phys. Commun., 2005)

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. - Haibo Yu 003; Daan P. Geerke; Haiyan Liu; Wilfred F. van Gunsteren (J. Comput. Chem., 2006)

Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues. - Haibo Yu 003; Liang Ma; Yang Yang; Qiang Cui (PLoS Comput. Biol., 2007)

Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations. - Haibo Yu 003; Liang Ma; Yang Yang; Qiang Cui (PLoS Comput. Biol., 2007)

A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function. - V. S. Sandeep Inakollu; Haibo Yu 003 (J. Comput. Chem., 2018)

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. - Ernest Awoonor-Williams; William C. Isley III; Stephen G. Dale; Erin R. Johnson; Haibo Yu 003; Axel D. Becke; Benoît Roux; Christopher N. Rowley (J. Comput. Chem., 2020)

Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. - Thomas M. Griffiths; Aaron J. Oakley; Haibo Yu 003 (J. Comput. Chem., 2020)

The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems. - Holden Paz; Silvan Beck; Richmond Lee; Junming Ho; Haibo Yu 003 (J. Comput. Chem., 2025)