Recent Publications

Some recent publications:

J. Spiriti & C.F. Wong, “Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning ”, Journal of Chemical Theory and Computation, (2024) .

C.F. Wong, “15 years of molecular simulation of drug-binding kinetics”, Expert Opinion on Drug Discovery, 18 (2023) 1333-1348.

Bao, X. Liu, R. Dou, S. Xu, D. Liu, J. Luo, X. Gong, C.F. Wong & B. Zhou, "How are N-methylcarbamates Encapsulated by β-cyclodextrin: Insights into the Binding Mechaism", Physical Chemistry Chemical Physics, 25 (2023) 13923-13932.

"" S. Rathnayake, B. Narayan, R. Elber, C.F. Wong, "Milestoning Simulation of Ligand Dissociation from the Glycogen Synthase Kinase 3 β", Proteins: Structure, Function, and Bioinformatics, 91 (2023) 209-217.

J. J. Spiriti, F. Noé, C.F. Wong, "Simulation of Ligand Dissociation Kinetics from the Protein Kinase PYK2", Journal of Computational Chemistry, 43 (2022) 1911-1922.

K. Chen, R. Ye, X. Liu, C.F. Wong, S. Xu, J. Luo, X. Gong, B., & B. Zhou, "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 (2021) 113496.

R. R. Dou, K. Chen, G. Chi, J. Luo, C.F. Wong, B. Zhou, “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 (2021) 189.

T. Chandak & C.F. Wong, “EDock-ML: A Web Server for Using Ensemble Docking with Machine Learning to Aid Drug Discovery”, Protein Science 30 (2021) 1087.

J. Spiriti & C.F. Wong, “Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics”, Life (Basel), 11 (2021) 74.

T. Chandak, J.P. Mayginnes, H. Mayes, C.F. Wong, "Using Machine Learning to Improve Ensemble Docking for Drug Discovery", Proteins: Structure, Function and Bioinformatics, 88 (2020) 1263.

C.F. Wong, "Improving Ensemble Docking for Drug Discovery by Machine Learning", Journal of Theoretical and Computational Chemistry 18 (2019) 192001.

H. Mayes & C.F. Wong, "Program for Simulating Gel Electrophoresis of Enzyme-Digested Proteins", Journal of Chemical Education, 95 (2018) 2064.

C.F. Wong, "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 (2018) 1307.

X. Nie, R. Ye, Y. Zhou, C.F. Wong, X. Gong, W. Jiang, W. Tang, Y.A. Wang, T. Heine & B. Zhou “Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach”, Chemical Physics Letters, 648 (2016) 170.

B. Zhou, X. Nie, R. Ye, C.F. Wong, X. Gong, Y. A. Wang & T. Heine, “Variable van der Waals radii derived from a hybrid Gaussian charge distribution model for continuum-solvent electrostatic calculations”, Zeitschrift für Physikalische Chemie, 230 (2016) 681.

C.F. Wong, "Progress in Pathogen Detection by Whole-Genome Sequencing", MOJ Proteomics & Bioinformatics, 3 (2016) 681.

Z. Huang & C.F. Wong, “An Inexpensive Method for Selecting Receptor Structures for Virtual Screening”, Journal of Chemical Information and Modeling, 56 (2016) 21.

C.F. Wong, “Incorporating Receptor Flexibility in Structure-Based Drug Discovery”, Method in Pharmacology and Toxicology, (2015) 65.

C.F. Wong, “Flexible Receptor Docking for Drug Discovery”, Expert Opinion on Drug Discovery, 10 (2015) 1189.

C.F. Wong, “Conformational Transition Paths Harbor Structures Useful for Aiding Drug Discovery and Understanding Enzymatic Mechanisms in Protein Kinases”, Protein Science, 25 (2016) 192.

C.F. Wong, "Incorporating Drug-Binding Kinetics in Drug Design" in: "In Silico Drug Discovery and Design: Theory, Methods, Challenges and Applications" C.N. Cavasotto (Ed.), CRC Press; 2015.

T. Shen & C.F. Wong, “Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program”, Methods in Molecular Biology,1268 (2015) 75.

M.P. Paudyal, L. Wu, Z.-Y. Zhang, C.D. Spilling & C.F. Wong, "A New Class of Salicylic Acid Derivatives for Inhibiting YopH of Yersinia pestis", Bioorg. Med. Chem., 22 (2014) 6781.

C.F. Wong, "Molecular Simulation of Drug-Binding Kinetics", Molecular Simulation, 40 (2014) 889.

P.M. Gontarz, J. Berger & C.F. Wong, "SRmapper: A Fast and Sensitive Genome-Hashing Alignment Tool", Bioinformatics, 29 (2013) 316.

C.F. Wong & S. Bairy, "Drug Design for Protein Kinases and Phosphatases: Flexible-Receptor Docking, Binding Affinity and Specificity, and Drug-Binding Kinetics", Current Pharmaceutical Design, 19 (2013) 4739.

Z. Huang & C.F. Wong, “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 (2012) 2275.

Z. Huang & C.F. Wong, “A Case Study of Scoring and Rescoring in Peptide Docking”, Methods in Molecular Biology, 819 (2012) 269-93.

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, 79 (2011) 2491–2504.

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 & 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.