Recent Publications

S. Bairy & C. F. Wong, “Influence of Kinetics of Drug Binding on EGFR Signaling: A Comparative Study of Three EGFR Signaling Pathway Models”, Proteins: Structure, Function, Bioinformatics, in press.

Z. Huang & C.F. Wong, “Incorporating Protein Flexibility in Molecular Docking by Molecular Dynamics: Applications to Protein Kinase and Phosphatase Systems” in “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, G. Zhang (Eds.), World Scientific, Singapore, London (2011) pp. 219-250.

J. Shi, Z. Lu, Q. Zhang, M. Wang, C.F. Wong and J. Liu, "Supplementing the PBSA approach with quantum mechanics to study the binding between CDK2 and N2-substituted O6-cyclohexylmethoxyguanine inhibitors", J. Theor. Comput. Chem., 9 (2010) 543.

Z. Huang, Y. He, X. Zhang, A. Gunawan, L. Wu, Z.-Y. Zhang & C. F. Wong, "Derivatives of Salicylic Acid as Inhibitors of YopH in Yersinia pestis", Chem. Biol. Drug Design, 76 (2010) 85-99.

Z. Huang & C.F. Wong, "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 (2009) 14343-14354.

M. Goyal, M. Rizzo, F. Schumacher & C.F. Wong, "Beyond Thermodynamics: Drug Binding Kinetics Could Influence Epidermal Growth Factor Signaling", J. Med. Chem., 52 (2009) 5582-5585.

B. Zhou & C.F. Wong, "A Computational Study of the Phosphorylation Mechansim of the Insulin Receptor Tyrosine Kinase", J. Phys. Chem. A, 30 (2009) 5144-5150.

Z. Huang & C.F. Wong, "Conformational Selection of Protein Kinase A Revealed by Flexible-Ligand Flexible-Protein Docking", J. Comput. Chem. 30 (2009) 631-644.

B. Zhou, M. Agarwal & C.F. Wong, “Variable Atomic Radii for Continuum-Solvent Electrostatics Calculation”, J. Chem. Phys. 129 (2008) 014509.

C.F. Wong, “Flexible Ligand-Flexible Protein Docking in Protein Kinase Systems”, Biochim Biophys Acta., 1784 (2008) 244-251.

Z. Huang, C.F. Wong & R. Wheeler, "Flexible Protein-Flexible Ligand Docking with Disrupted Velocity Simulated Annealing", Proteins: Structure, Function, Bioinformatics, 7 (2008) 440-454.

Z. Huang & C.F. Wong, "A Mining-Minima Approach to Exploring the Docking Pathways of p-Nitrocatechol Sulfate to YopH", Biophys. J.,  83 (2007) 4141-4150.

M. Wang, C. F. Wong, J. Liu & P. Zhang, "Efficient Quantum Mechanical Calculation of Solvation Free Energies Based on Density Functional Theory, Numerical Atomic Orbitals and Poisson–Boltzmann Equation", Chem. Phys. Lett., 442 (2007) 464-467.

M. Wang & C.F. Wong, "Rank-ordering Protein-Ligand Binding Affinity by a QM/MM/PBSA Model", J. Chem. Phys., 126 (2007) 026101.

M. Wang & C.F. Wong, “Calculation of Solvation Energy from Quantum Mechanical Charge Density and Continuum Dielectric Theory”, J. Phys. Chem. A, 110 (2006) 4873-4879.

C. Wang & C.F. Wong, "Molecular Dynamics Simulation of Laser Desorption of a Fragment of Protein Kinase A from two MALDI Matrices", J. Phys. Chem. A, 110 (2006) 5355-5360.

B. Lu & C.F. Wong, "Direct Estimation of Entropy Loss due to Reduced Translational and Rotational Motions upon Molecular Binding", Biopolymers 79 (2005) 277-285.

C.F. Wong, J. Kua, Y.-K. Zhang, T. Straastma & J. A. McCammon, “Docking of Balanol to Dynamics Snapshots of Protein Kinase A”, Proteins: Structure, Function, Bioinformatics 61 (2005) 850-858.

P. Sims, C.F. Wong, D. Vuga, J.A. McCammon & B. M. Sefton, “Relative Contribtuions of Desolvation, Inter-, and Intramolecular Interactions to Binding Affinity in Protein Kinase Systems”, J. Comput. Chem. 26 (2005) 668-681.

B.Z. Lu, C.F. Wong & J.A. McCammon, “Release of ADP from the Catalytic Subunit of Protein Kinase A: A Molecular Dynamics Simulation Study”, Protein Sci. 14 (2005) 159-168.

S. Senapati, C.F. Wong & J.A. McCammon, “Finite Concentration Effects on Diffusion-controlled Reactions”, J. Chem. Phys. 121 (2004) 7896-7900.

P. Sims, C.F. Wong & J.A. McCammon, “Charge Optimization of the Interface between Protein Kinases and their Ligands”, J. Comput. Chem. 25 (2004) 1416-1429.

C.F. Wong & J. A. McCammon, “Drug Design”, in “Encyclopedia of   Supramolecular Chemistry” Jerry L. Atwood & Jonathan W. Steed (Eds.), Marcel Dekker, Inc., New York (2004), pp. 490-496.

D. Cerutti, C.F. Wong & J.A. McCammon, “Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric”, Biopolymers 70 (2003) 391-402.

P. Sims, C.F. Wong & J.A. McCammon, “A Computational Model of Binding Thermodynamics: The Design of CDK2 Inhibitors”, J. Med. Chem. 46 (2003) 3314-3325.

K. Toendel, C.F. Wong & J.A. McCammon, “Computational Analysis of the Interactions between the Angiogenesis Inhibitor PD173074 and Fibroblast Growth Factor Receptor 1”, J. Theo. Comput. Chem. 2 (2003) 43-56.

T. Shen, C.F. Wong & J.A. McCammon, “Brownian Dynamics Simulation of Helix-Capping Motifs”, Biopolymers 70 (2003) 252-259.

C.F. Wong & J.A. McCammon, “Protein Simulation and Drug Design”, Adv Protein Chem 66 (2003) 87-121.

C.F. Wong & J.A. McCammon, “Protein flexibility and computer-aided drug design”, Annu. Rev. Pharmacol. Toxicol. 43 (2003) 31-45.

G. Gidofalvi, C.F. Wong & J.A. McCammon, “Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A”, J. Chem. Edu. 79 (2002) 1122-1126.

C. Gould & C.F. Wong, “Designing Specific Protein Kinase Inhibitors: Insights from Computer Simulations and Comparative Sequence/Structure Analysis”, Pharmacology & Therapeutics 93 (2002) 169-178.

T. Shen, C.F. Wong & J.A. McCammon, “Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation”, J. Amer. Chem. Soc. 123 (2001) 9107.

B. Nolen, C.Y. Yun, C.F. Wong, J.A. McCammon, X.D. Fu & G. Ghosh, “The Structure of Sky1p Reveals a Novel Mechanism for Constitutive Activity”, Nature Struct. Biol. 8 (2001) 176-183.

C.F.Wong, Philippe H. Hünenberger, Pearl Akamine, Narendra Narayana, Tom Diller,  J. Andrew McCammon, Susan Taylor & Nguyen-Huu Xuong, “Computational Analysis of PKA-Balanol Interactions”, J. Med. Chem. 44 (2001) 1530-1539.