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.
Chandak, T. and C. F. Wong (2021). "EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery." Protein Science 30(5): 1087-1097.
Chandak, T., J. P. Mayginnes, H. Mayes and C. F. Wong (2020). "Using machine learning to improve ensemble docking for drug discovery." Proteins: Structure, Function and Bioinformatics 88(10): 1263-1270.
Wong, C. F. (2019). "Improving ensemble docking for drug discovery by machine learning." Journal of Theoretical and Computational Chemistry 18(3).
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.
Wong, C. F. (2016). "Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases." Protein Science 25(1): 192-203.
Paudyal, M. P., L. Wu, Z. Y. Zhang, C. D. Spilling and C. F. Wong (2014). "A new class of salicylic acid derivatives for inhibiting YopH of Yersinia pestis." Bioorganic and Medicinal Chemistry 22(24): 6781-6788.
Wong, C. F. and S. Bairy (2013). "Drug design for protein kinases and phosphatases: Flexible-receptor docking, binding affinity and specificity, and drug-binding kinetics." Current Pharmaceutical Design 19(26): 4739-4754.
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.
Bairy, S. and C. F. Wong (2011). "Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models." Proteins: Structure, Function and Bioinformatics 79(8): 2491-2504.
Shi, J., Q. Lu, M. Zhang, M. Wang, C. F. Wong and J. Liu (2010). "Supplementing the PBSA approach with quantum mechanics to study the binding between CDK2 and N2-substituted O6-cyclohexylmethoxyguanine inhibitors." J. Theor. Comput. Chem. 9: 543-559.
Huang, Z., Y. He, X. Zhang, A. Gunawan, L. Wu, Z. Y. Zhang and C. F. Wong (2010). "Derivatives of salicylic acid as inhibitors of YopH in Yersinia pestis." Chem Biol Drug Des 76(2): 85-99.
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. 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.
Zhou, B. and C. F. Wong (2009). "A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase." J Phys Chem A 113(17): 5144-5150.
Goyal, M., M. Rizzo, F. Schumacher and C. F. Wong (2009). "Beyond thermodynamics: drug binding kinetics could influence epidermal growth factor signaling." J Med Chem 52(18): 5582-5585.
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.
Wong, C. F. (2008). "Flexible ligand-flexible protein docking in protein kinase systems." Biochimica Et Biophysica Acta-Proteins and Proteomics 1784(1): 244-251.
Wang, M. L. and C. F. Wong (2007). "Rank-ordering protein-ligand binding affinity by a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model." Journal of Chemical Physics 126(2): 026101.
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.
Straatsma, T. P., J. A. McCammon, J. H. Miller, P. E. Smith, E. R. Vorpagel, C. F. Wong and M. Zacharias (2006). Simulation of Base Excision Repair and Protein Signaling. U. S. D. o. E. T. R. #PNNL-15687.
Wong, C. F., J. Kua, Y. Zhang, T. P. Straatsma and J. A. McCammon (2005). "Molecular docking of balanol to dynamics snapshots of protein kinase A." Proteins 61(4): 850-858.
Sims, P. A., C. F. Wong, D. Vuga, J. A. McCammon and B. M. Sefton (2005). "Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems." J Comput Chem 26(7): 668-681.
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.
Sims, P., C. Wong and J. McCammon (2004). "Charge optimization of the interface between protein kinases and their ligands." JOURNAL OF COMPUTATIONAL CHEMISTRY 25(11): 1416-1429.
Toendel, K., C. F. Wong and J. A. McCammon (2003). "Computational Analysis of the Interactions between the Angiogenesis Inhibitor PD173074 and Fibroblast Growth Factor Receptor 1." J Theor Comput Chem 2(1): 43-56.
Sims, P., C. F. Wong and J. A. McCammon (2003). "A Computational Model of Binding Thermodynamics: The Design of CDK2 Inhibitors." J Med Chem 46(15): 3314-3325.
Gould, C. and C. F. Wong (2002). "Designing specific protein kinase inhibitors: insights from computer simulations and comparative sequence/structure analysis." Pharmacology and Therapeutics 93(2-3): 169-178.
Gidofalvi, G., C. F. Wong and J. A. McCammon (2002). "Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A." J. Chem. Ed. 79(9): 1122-1126.
Wong, C. F., P. H. Hünenberger, P. Akamine, N. Narayana, T. Diller, J. A. McCammon, S. Taylor and N. H. Xuong (2001). "Computational analysis of PKA-balanol interactions." Journal of Medicinal Chemistry 44(10): 1530-1539.
Shen, T. Y., C. F. Wong and J. A. McCammon (2001). "Atomistic Brownian dynamics simulation of peptide phosphorylation." Journal of the American Chemical Society 123(37): 9107-9111.
Nolen, B., C. Y. Yun, C. F. Wong, J. A. McCammon, X. D. Fu and G. Ghosh (2001). "The structure of Sky1p reveals a novel mechanism for constitutive activity." Nature Structural Biology 8(2): 176-183.