Zhang D., Gullingsrud J. & McCammon JA (2006) Potentials of Mean Force for Acetylcholine Unbinding from the Alpha7 Nicotinic Acetylcholine Receptor Ligand-Binding Domain J Am Chem Soc 108(9):3019-26

Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL 3rd, McCammon JA (2006) Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, In press.

McClendon CL, Vaidehi N, Kam VWT, Zhang D, Goddard WA (2006) Fidelity of Seryl-tRNA Synthetase to Binding of Natural Amino Acids from HierDock First Principles Computations. Protein Engineering, Design, and Selection. In press

Zhang, D. & Mccammon JA (2005) The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput Biol 1(6): e62

Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. (2005) Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical Journal 88:1659-1665.

Lu B, Zhang D, McCammon JA. (2005) Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys. 122(21):214102

Zhang D, Konecny R, Baker NA, McCammon JA. (2004) Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers. 75(4):325-37.

Deepshikha Datta, Nagarajan Vaidehi, Deqiang Zhang, William A. Goddard III, 2004, Selectivity and specificity of ligand binding in methionyl-tRNA synthetase. Protein Science, 13(10), 2693-2705.

Patrick L. Wintrode^*, Deqiang Zhang^*, Nagarajan Vaidehi, Frances H. Arnold & William A. Goddard III, 2003, Molecular Dynamics study of a family of laboratory evolved thermophilic enzymes. J. Mol. Biol. 327(3), 745-757.  *Equal authorship

Deqiang Zhang, Nagarajan Vaidehi, William A. Goddard III, Joseph Danzer & Derek Debe, 2002, Structure-Based Design of Mutant Methanococcus jannaschii Tyrosyl-tRNA Synthetase for Incorporation of O-Methyl-L-Tyrosine. Proc. Natl. Acad. Sci. 99(10), 6579-6584.

Dongping Zhong, Samir Kumar Pal, Deqiang Zhang, Sunney I. Chan & Ahmed H. Zewail, 2002, Femtosecond Dynamics of Rubredoxin: Tryptophan Solvation and Resonance Energy Transfer in the Protein. Proc. Natl. Acad. Sci. 99(1), 13-18.

Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics of the reaction of hydroxyl radicals with CH2Br2 and its implications in the atmosphere, J. Atmos. Chem., 27(2), 209-215.

Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants for the reaction of hydroxyl radicals with HFC-134A, J. Environ. Sci., 9(3), 361-365.

Deqiang Zhang, & Jinxian Zhong, 1997, The estimation of the ODP values for CH3Br and CH2Br2, Chinese J. Environ. Sci., 17(3).

Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics for the reaction of hydroxyl radicals with CH₃Br and its implications in the atmosphere, J. Environ. Sci ., 9(4), 480-485.

Jinxian Zhong & Deqiang Zhang, 1997, Characterization of the photo-oxidization of CH₃Br and CHBr₃ in the presence of H₂O₂, Chinese J. Environ. Sci., 17(2).

Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants of the reaction of hydroxyl radicals with C₂H₅Br and the tropospheric lifetime of C₂H₅Br, Chinese J. Environ. Sci., 17(4).

Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen, Shuqin Yu, & Xingxiao Ma, 1994, Laser-induced fluorescence spectrum of PH2 radicals cooled in a supersonic free jet, Chem. Phys. Lett., 223(1-2), 104-109.

Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen & Xingxiao Ma, 1993, The LIF spectrum of PH₂ radicals cooled in a supersonic free jet, Chinese J. Chem. Phys., 6(5), 426-433.