Our research frequently employs computational approaches to help us understand the chemical and biochemical properties of biomolecules, from drugs to proteins and materials. Many of our papers have employed molecular mechanics, semi-empirical, ab initio, and density functional theory calculations, as well as molecular dynamics simulations. The following are journal articles where theoretical investigations are an important contribution or the sole focus of the research.
M. Lopandic, F. Merza, and J. F. Honek, 2023, Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues. Compounds, 3, 464-503.
A. M. van der Ven, H. Gyamfi, U. Suttisansanee, M. S. Ahmad, Z. Su, R. M. Taylor, A. Poole, S. Chiorean, E. Daub, T. Urquhart, and J. F. Honek, 2023, Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules, 28(12), 4663.
C. Ieritano, D. Rickert, J. Featherstone, J. Honek, L. Campbell, Y. J. C. Le Blanc, B. Schneider, and W. Hopkins, 2021, The Charge-State and Structural Stability of Peptides Conferred by Microsolvating Environments in Differential Mobility Spectrometry. Journal of the American Society of Mass Spectrometry, 32(4), 956-968.
M. Lu, Q-B. Lu and J. F. Honek, 2017, Squarate-Based Carbocyclic Nucleosides: Syntheses, Computational Analyses and Anticancer/Antiviral Evaluation. Bioorganic and Medicinal Chemistry Letters, 27, 282-287.
U. Suttisansanee and J. F. Honek, 2017, Hydroxamate Inhibitor Profiling of Both Zn2+- and Ni2+-Activated Glyoxalase I Metalloenzymes Having Diverse Quaternary Structures. Letters in Drug Design and Discovery, 14, 843-852.
I. A. Moya, G. D. Westrop, G. H. Coombs and J. F. Honek, 2011, Mechanistic Studies on the Enzymatic Processing of Fluorinated Methionine Analogs by Trichomonas vaginalis Methionine γ-Lyase. Biochemical Journal, 438, 513-521.
Z. Su, K. Mui, E. Daub, T. Leung and J. F. Honek, 2007, Single-walled Carbon Nanotube Binding Peptides: Probing Tryptophan's Importance by Unnatural Amino Acid Substitution. J. Phys. Chem. B, 111, 14411-14417.
M. D. Vaughan, V. J. Robertson and J. F. Honek, 2007, Experimental and theoretical studies on inversion dynamics of dichloro(L-difluoromethionine -N,S)platinum(II) and dichloro(L-trifluoromethionine-N,S)platinum(II) complexes. J. Fluorine Chem., 128, 65-70.
C. E. Hand and J. F. Honek, 2007, Phosphate Transfer from Inositol Pyrophosphates InsP5PP and InsP4(PP)2: A Semi-empirical Investigation. Bioorg. Med. Chem. Lett., 17, 183-188.
C. E. Hand, F.-I. Auzanneau and J. F. Honek, 2006, Conformational Analyses of Mycothiol, a Critical Intracellular Glycothiol in Mycobacteria. Carbohydrate Research, 341, 1164-1173.
P. C. Hang and J. F. Honek, 2005, Electronic Structure Calculations on the Thiazole-Containing Antibiotic Thiostrepton: Molecular Mechanics, Semi-Empirical and Ab initio Analyses. Bioorganic and Medicinal Chemistry Letters, 15, 1471-1474.
C. E. Hand, N. J. Taylor and J. F. Honek, 2005, Ab Initio Studies of the Properties of Intracellular Thiols Ergothioneine and Ovothiol. Bioorganic and Medicinal Chemistry Letters, 15, 1357-1360.