Spiriti, J. and C. F. Wong (2024). "Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning." Journal of Chemical Theory and Computation 20(9): 4029-4044.
Rathnayake, S., B. Narayan, R. Elber and C. F. Wong (2023). "Milestoning simulation of ligand dissociation from the glycogen synthase kinase 3β." Proteins: Structure, Function and Bioinformatics 91(2): 209-217.
Spiriti, J., F. Noé and C. F. Wong (2022). "Simulation of ligand dissociation kinetics from the protein kinase PYK2." Journal of Computational Chemistry 43(28): 1911-1922.
Spiriti, J. and C. F. Wong (2021). "Qualitative prediction of ligand dissociation kinetics from focal adhesion kinase using steered molecular dynamics." Life 11(2): 1-19.
Dou, R., K. Chen, G. Chi, J. Luo, C. F. Wong and B. Zhou (2021). "Why heptakis(2,3-di-O-acetyl)-β-cyclodextrin can separate terbutaline enantiomers better than β-cyclodextrin: nonbonding and hydrophobic interactions." Journal of Inclusion Phenomena and Macrocyclic Chemistry 100(3-4): 189-195.
Chen, K., R. Ye, X. Liu, C. F. Wong, S. Xu, J. Luo, X. Gong and B. Zhou (2021). "Why 2,6-di-methyl-β-cyclodextrin can encapsulate OH-substituted naphthalenes better than β-cyclodextrin: Binding pose, non-covalent interaction and solvent effect." Computational and Theoretical Chemistry 1206.
Wong, C. F. (2018). "Steered molecular dynamics simulations for uncovering the molecular mechanisms of drug dissociation and for drug screening: A test on the focal adhesion kinase." Journal of Computational Chemistry 39(19): 1307-1318.
Huang, Z. and C. F. Wong (2012). "A Case Study of Scoring and Rescoring in Peptide Docking." Methods in Molecular Biology 819: 269-293.
Huang, Z. and C. F. Wong (2012). "Simulation reveals two major docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor protein kinase." Proteins: Structure, Function and Bioinformatics 80(9): 2275-2286.
Huang, Z. and C. F. Wong (2011). Incorporating Protein Flexibility in Molecular Docking by Molecular Dynamics. Computational Studies of New Materials II: From Ultrafast Processes and Nanostructures to Optoelectronics, Energy Storage and Nanomedicine. T. F. George, D. Jelski, R. R. Letfullin and G. Zhang. Singapore, London, World Scientific: 219-250.
Huang, Z. and C. F. Wong (2009). "Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems." J Phys Chem B 113(43): 14343-14354.
Huang, Z. and C. F. Wong (2009). "Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking." Journal of Computational Chemistry 30(4): 631-644.
Huang, Z., C. F. Wong and R. A. Wheeler (2008). "Flexible protein-flexible ligand docking with disrupted velocity simulated annealing." Proteins 71(1): 440-454.
Huang, Z. and C. F. Wong (2007). "A mining minima approach to exploring the docking pathways of p-nitrocatechol sulfate to YopH." Biophys J 93(12): 4141-4150.
Wang, C. and C. F. Wong (2006). "Molecular dynamics simulation of laser desorption of a fragment of protein kinase A from two maldi matrices." Journal of Physical Chemistry A 110(16): 5355-5360.
Lu, B., C. F. Wong and J. A. McCammon (2005). "Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study." Protein Science 14(1): 159-168.
Wang, Q., C. F. Wong and H. Rabitz (1998). "Simulating energy flow in biomolecules: Application to tuna cytochrome c." Biophysical Journal 75(1): 60-69.
Simonson, T., C. F. Wong and A. T. Brünger (1997). "Classical and quantum simulations of tryptophan in solution." J. Phys. Chem. A 101: 1935-1945.
Zhu, S.-B. and C. F. Wong (1994). "Sensitivity Analysis of a Polarizable Water Model." J. Phys. Chem. 98(17): 4695-4701.
Zhu, S.-B. and C. F. Wong (1993). "Sensitivity Analysis of Water Thermodynamics." J. Chem. Phys. 98(11): 8892-8899.
Zhu, S.-B. and C. F. Wong (1993). "Sensitivity Analysis of Distribution Functions of Liquid Water." J. Chem. Phys. 99(11): 9047-9053.
Wong, C. F., C. Zheng, J. Shen, J. A. McCammon and P. G. Wolynes (1993). "Cytochrome c: a molecular proving ground for computer simulations." J. Phys. Chem. 97(13): 3100-3110.
Wong, C. F. and H. Rabitz (1991). "Sensitivity Analysis and Principal Component Analysis in Free Energy Calculations." J. Phys. Chem. 95(24): 9628-9630.
Wong, C. F. (1991). "Systematic Sensitivity Analyses in Free Energy Perturbation Calculations." J. Am. Chem. Soc. 113: 3208-3209.
Zheng, C., C. F. Wong and J. A. McCammon (1990). "Fluctuation of the solvent-accessible surface area of tuna ferrocytochrome c." Biopolymers 29: 1877-1883.
Shen, J., C. F. Wong and J. A. McCammon (1990). "Hydration of superoxide studied by molecular dynamics simulation." J. Comp. Chem. 11(8): 1003-1008.
Zheng, C., C. F. Wong, J. A. McCammon and P. G. Wolynes (1989). "Quantum Effects in Protein Dynamics." Chemica Scripta 29A: 171-179.
Wong, C. F., C. Zheng and J. A. McCammon (1989). "Glass transition in SPC/E water and in a protein solution: a molecular dynamics study." Chem. Phys. Lett. 154(2): 151-154.
Wong, C. F., J. Shen, C. Zheng, S. Subramaniam and J. A. McCammon (1989). "Molecular dynamics simulation of protein hydration: studies on tuna ferrocytochrome-c and bovine erythrocyte superoxide dismutase." J. Mol. Liq. 41: 193-206.
Shen, J., S. Subramaniam, C. F. Wong and J. A. McCammon (1989). "Superoxide dismutase: fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation." Biopolymers 28: 2085-2096.
McCammon, J. A., C. F. Wong and T. P. Lybrand (1989). Protein Stability and Function: Theoretical Studies. Prediction of Protein Structure and Protein Conformation. G. D. Fasman. New York Plenum: 149-159.
Zheng, C., C. F. Wong, J. A. McCammon and P. G. Wolynes (1988). "Quantum simulation of ferrocytochrome c." Nature 334(6184): 726-728.
Wong, C. F. and J. A. McCammon (1988). Molecular Dynamics Simulation Studies of Water and Protein Solutions. Science on the ETA10. L. Anacker. Princeton, NJ, John von Neumann Center: 61-66.
McCammon, J. A., G. Ganti, T. P. Lybrand and C. F. Wong (1988). Supercomputer Simulation and Biomolecular Design. High Speed Computing, Scientific Applications and Algorithm Design. R. B. Wilhelmson, University of Illinois Press: 155-161.
Wong, C. F. and J. A. McCammon (1987). Protein-Water Surface Interactions: A Biomolecular Dynamics Simulation. Science at the John von Neumann Center, 1987. L. Anacker. Princeton, NJ John von Neumann Center: 131-134.
Wong, C. F. and J. A. McCammon (1986). "Computer simulation and the design of new biological molecules." Isr. J. Chem. 27: 211-215.
Wong, C. F. and J. A. McCammon (1986). Thermodynamics of Enzyme Folding and Activity: Theory and Experiment. Structure, Dynamics and Function of Biomolecules. A. Ehrenberg and R. Rigler. Berline, Springer-Verlag: 51-55.
Wong, C. F. and J. A. McCammon (1986). "Dynamics and design of enzymes and inhibitors." J. Am. Chem. Soc. 108(13): 3830-3832.