Recent Publications (2001-)

64. Z. Huang & C.F. Wong, "Conformational Selection of Protein Kinase A Revealed by Flexible-Ligand Flexible-Protein Docking", J. Comput. Chem. (2008).

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

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

61. 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.

60. 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.

59.  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.

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

57.  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.

56.  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.

55.  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.

54.  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.

53.  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.

52.  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.

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

50.  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.

49.  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.

48.  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.

47.  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.

46.  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.

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

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

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

42.  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.

41.  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.

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

39.  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.

38.  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.