Publications

• Katpally, S.; Ghorab, M. K., Madura, J. D., Mosher, J., Thompson, D., Adeyeye, M. C. Characterization of Bile Salt/SBE-7 b -cyclodextrin Interactions Using Isothermal Titration Calorimetry (submitted).
• Thomas, L.L., Dalal, P.D., Aronson, N.N.Jr., Madura, J.D. Molecular Modeling of b (1 à 4) linked N-acetyl glucosamine in SmChiA Subsites, J. Chem. Info. Comput. Sci. (submitted).
• Dalal, P.D., Robertson, K, Aronson, N.N.Jr., Madura, J.D. Isothermal Calorimetric Study of Oligosaccharide Binding to SmChiA E315L Mutant, FEBS Letts. (submitted).
• Dalal, P.D., Robertson, K, Aronson, N.N.Jr., Madura, J.D. Fluorescence Study of Oligosaccharide Binding to SmChiA E315L Mutant, FEBS Letts. (submitted).
• Dalal, P.; Thomas, L. L.*; Robertson, K.*; Halloran, B. A.; Aronson Jr., N. N.; Madura , J.D. Thermodynamic properties of chitinase interaction with chitohexaose2004, (submitted)
• Dalal, P.; Zanotti, K. Wierzbicki, A; Madura, J. D. Lipid bilyar simulations, Biophysics J.(2005), (in press). [Epub ahead of print]
• Dick, Thomas J.; Madura, Jeffry D A Review of TIP4P: TIP4P-Ew, TIP5P and TIP5P-E Water ModelsAnnual Reports in Computational Chemistry (2005), 1, 59-74.
• Berberich, Jason, A.; Yang, Lee, W.; Madura, Jeffry D.; Bahar, I. and Russell, Alan, J. A stable three-enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase ActaBiomaterialia(2005), 1, 173-181.
• Zhou, Zhigang; Madura, Jeffry D Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS Proteins: Structure, Function, and Bioinformatics (2004), 57(3), 493-503 [pdf]
• Esposito, Emilio Xavier; Hopfinger, Anton J.; Madura, Jeffry D Methods for applying the quantitative structure-activity relationship paradigm Methods in Molecular Biology (2004), 275(Chemoinformatics), 131-213.
• Horn, Hans W.; Swope, William C.; Pitera, Jed W.; Madura, Jeffry D.; Dick, Thomas J.; Hura, Greg L.; Head-Gordon, Teresa. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew Journal of Chemical Physics (2004), 120(20), 9665-9678.
• Zhou, Z.; Madura, J. D. CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment (2004)J. Chem. Infor. Comput. Sci. 44, 2167-2178.
• Nunes, S.; Zhou, Z.; Evanseck, J. D.; Madura, J. D. Computational analysis of Cadmium Sulfide (CdS) Nanocrystals” Encyclopedia of Nanoscience and Nanotechnology (2004), MarcelDekker Inc.
• Aronson, Nathan N., Jr.; Halloran, Brian A.; Alexyev, Mikhail F.; Amable, Lauren; Madura, Jeffry D.; Pasupulati, Lakshminarasimhulu; Worth, Catherine; Van Roey, Patrick. Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A. Biochemical Journal (2003), 376(1), 87-95.
• Wierzbicki, A.; Dalal, P.; Madura, J.D. Molecular Dynamics Simulations of Crystal Induced Membranolysis J. Phys. Chem. B ( 2003),107, 12345-12351.
• Zhou, Zhigang; Fisher, Derek; Spidel, Jared; Greenfield, Jodi; Patson, Brian; Fazal, Aleem; Wigal, Carl; Moe, Owen A.;Madura, Jeffry D. Kinetic and Docking Studies of the Interaction of Quinones with the Quinone Reductase Active Site. Biochemistry. (2003), 42, 1985-1994.
• Madura, Jeffry D.; Salter, Edward A.; Wierzbicki, Andrzej; Dalal, Pranav; Harrington, John P. Homology Models for the Tetrameric and Dodecameric Complexes of Lumbricus terresitris Hemoglobin. Theochem. (2002), 592, 173-181.
• Walsh, Mary Beth; Moss, Connie M.; Johnson, Benny G.; Holder, Dale A.; Madura, Jeffry D.. Quantitative of a cognitive modeling intelligent tutoring system on student performance in balancing chemical equations. Chemical Educator (2002), 7(6), 379-383.
• Zhou, Zhigang; Madrid, Marcela; Madura, Jeffry D. Docking of Non-nucleoside Inhibitors: Neotripterifordin and its Derivatives to HIV-1 Reverse Transcriptase, Proteins: Structure, Function, and Genetics. (2002), 49, 529-541.
• Carlier, Paul R.; Madura, Jeffry D., Effective Computational Modeling of Constitutional Isomerism and Aggregation States of Explicit Solvates of Lithiated Phenylacetonitrile. Journal of Organic Chemistry (2002), 67 (11), 3832-3840.
• Dick, Thomas J.; Acevedo, Orlando; Dalal, Pranav; Madura, Jeffry D.; Evanseck, Jeffrey D.; Mathews, Jonathan P. Molecular Basis For Carbon Dioxide Sequestration In Coal. Reprints of Symposia-American Chemical Society, Division of Fuel Chemistry (2002), 47(1), 14-16.
• Lakshminarasimhulu, Pasupulati; Madura, Jeffry D. A Cell Multipole Based Domain Decomposition Algorithm For Molecular Dynamics Simulation of Systems of Arbitrary Shape. Computer Physics Communications (2002), 144(2), 141-153.
• Esposito, Emilio Xavier; Baran, Kelli; Kelly, Ken; Madura, Jeffry D. Docking Substrates To Metalloenzymes. Molecular Simulation (2001), 24(4-6), 293-306.
• Madrid, Marcela; Lukin, Jonathan A.; Madura, Jeffry D.; Ding, Jianping; Arnold, Edward. Molecular Dynamics of HIV-1 Reverse Transcriptase Indicates Increased Flexibility Upon DNA Binding. Proteins: Structure, Function, and Genetics (2001), 45(3), 176-182.
• Dalal, Pranav; Knickelbein, Jared; Haymet, A.D.J.; Sonnichsen, Frank D.; Madura, Jeffry D. Hydrogen Bond Analysis of Type 1 Antifreeze Protein in Water and the Ice/Water Interface. PhyChem Comm (online computer file) (2001), Paper No. 7.
• Harris, Michael N.; Madura, Jeffry D.; Ming, Li-June; Harwood, Valerie J. Kinetic and Mechanistic Studies of Prolyl Oligopeptidase from the Hyperthermophile Pyrococcus Furiosus. Journal of Biological Chemistry (2001), 276(22), 19310-19317. [pdf]
• Ravichandran, S.; Madura, Jeffry D.; Talbot, J. A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface. Journal of Physical Chemistry B (2001), 105(17), 3610-3613.
• Spreitzer, Glen; Whitling, Jacqueline M.; Madura, Jeffry D.; Wright, David W. Peptide-encapsulated CdS Nanoclusters from a Combinatorial Ligand Library. Chemical Communications (Cambridge) (2000), (3), 209-210.
• Esposito, E.X.; Baran, K.; Kelly, K.; Madura, J.D. Docking of Sulfonamides To Carbonic Anhydrase II and IV. Journal of Molecular Graphics & Modelling (2000), 18(3), 283-289.
• Madura, Jeffry D.; Baran, Kelli; Wierzbicki, Andrzej. Molecular Recognition and Binding of Thermal Hysteresis Proteins to Ice. Journal of Molecular Recognition. (2000), 13(2), 101-113.
• Madura, J. D.; Lombardini, J.B.; Briggs, J.M.; Minor, D.L.; Wierzbicki, A. Physical and Structural Properties of Taurine and Taurine Analogues. Amino Acids (1997), 13(2), 131-139.
• Aronson, Nathan N.; Blanchard, Christopher, J.; Madura, Jeffry D. Homology Modeling of Glycosyl Hydrolase Family 18 Enzymes and Proteins. Journal of Chemical Information and Computer Sciences (1997), 37(6), 999-1005.
• Wierzbicki A.; Madura, Jeffry D.; Salmon, C.; Sonnichsen, F. Modeling Studies of Binding of Sea Raven Type II Antifreeze Protein to Ice. Journal of Chemical Information and Computer Sciences (1997), 37(6), 1006-10.
• Wierzbicki, A.; Taylor, M.S.; Knight, C.A.; Madura, J.D.; Harrington, J.P.; Sikes, C.S. Analysis of Shorthorn Sculpin Antifreeze Protein Stereospecific Binding To (2-1 0) Faces of Ice. Biophysics Journal (1996), 71(1), 8-18.
• Wierzbicki, Andrzej; Salter, Edward A.; Hoffman, Norris W.; Stevens, Edwin D.; Van Do, Liem; VanLoock, Margaret S.; Madura, Jeffry D. Structural Investigations of trans-Rh(PY3)2(CO)X (X=F, CI, NCO; Y=H, Me, Ph) Using Density Functional Theory and X-ray Analysis. Journal of Physical Chemistry (1996), 100(27), 11250-11254.
• Huang, Ching-Li; Harrison, B. Keith; Madura, Jeffry; Dolfing, Jan. Gibbs Free Energies of Formation of PCDDs: Evaluation of Estimation Methods and Application For Predicting Dehalogenation Pathways. Environ. Toxicol. and Chem. (1996), 15(6), 824-836.
• Madura, Jeffry D.; Nakajima, Yasushi; Hamilton, Rodney M.; Wierzbicki, Andrzej; Warshel, Arieh. Calculations of the Electrostatic Free Energy Contributions to the Binding Free Energy of Sulfonamides to Carbonic Anhydrase. Struct. Chem. (1996), 7(2), 131-138.
• Davis, James H., Jr.; Madura, Jeffry D. Synthesis and Computational Evaluation of a Boronium Ion Analogue of the Tropane Ring System. Tetrahedron Lett. (1996), 37(16), 2729-30.
• Madura, Jeffry D.; Taylor, Mark S.; Wierzbicki, Andrzej; Harrington, John P.; Sikes, C.S.; Sooennichsen, Frank. The Dynamics and Binding Of A Type III Antifreeze Protein In Water And On Ice. THEOCHEM (1996), 388 65-77.
• Madura, Jeffry D.; Briggs, James M.; Wade, Rebecca C.; Davis, Malcolm E.; Luty, Brock A.; Llin, Andrew; Antosiewicz, Jan; Gilson, Michael K.; Bagherri, Babak; et al. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. (1995), 91-(1-3), 57-95.
• Gilson, Michael, K.; McCammon, J. Andrew; Madura, Jeffry D. Molecular Dynamics Simulation With A Continuum Electrostatic Model of the Solvent. Journal of Computational Chemistry (1995), 16(9), 1081-95.
• Young, Sidney, H.; Madura, Jeffry D.; Wierzbicki, Andrzej. Integration of Numerical Methods Into The Undergraduate Physical Chemistry Curriculum Using MATHCAD. J. Chem. Educ. (1995), 72(7), 609-10.
• Schaffer, S. W.; Azuma, J.; Madura, J.D. Mechanisms Underlying Taurine-Mediated Alterations In Membrane Function. Amino Acids (1995), 8(3), 231-46.
• Wierzbicki, A.; Sikes, C.S.; Sallis, J.D.; Madura, J.D.; Stevens, E.D.; Martin, K.L. Scanning Electron Microscopy and Molecular Modeling of Inhibition of Calcium Oxalate Monohydrate Crystal Growth by Citrate and Phosphocitrate. Calcified Tissue International (1995), 56(4), 297-304.
• Wierzbicki, A.; Sikes, C. S.; Madura, J. D.; Drake, B. Atomic Force Microscopy and Molecular Modeling of Protein and Peptide Binding to Calcite. Calcified Tissue International (1994), 54, 133-141.
• Madura, J. D.; Wierzbicki, A.; Harrington, J. P.; Maughon, R. H.; Raymond, J. A.; Sikes, C. S. Interactions of the D and L Forms of Winter Flounder Antifreeze Peptide with the {201} Planes of Ice. J. Amer. Chem. Soc. (1994), 116, 417-418.
• Salter, E. A.; Wierzbicki, A.; Seminario, J. M.; Hoffman, N. W.; Easterling, M. L.; Madura, J. D. The Structure of trans-Rh(PH3)2(CO)X (X=F, Cl) Using Hartree-Fock/MBPT(2) Theory and Density Functional Theory. J. Phys. Chem. (1994), 98, 12945-12948.
• Wade, Rebecca C.; Luty, Brock A.; Demchuk, Eugene; Madura, Jeffry D.; Davis, Malcolm, E.; Briggs, James M.; McCammon, J.Andrew. Simulation of Enzyme-Substrate Encounter With Gated Active Sites. Struct. Biol. (1994), 1(1), 65-9.
• Wade, Rebecca C.; Davis, Malcolm E.; Luty, Brock A.; Madura, Jeffry D.; McCammon, J. Andrew. Department Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys. J. (1993), 64(1), 9-15.
• Cannon, William R.; Madura, Jeffry D.; Thummel, Randolph P.; McCammon, J. Andrew. Molecular Recognition: Effect of Rotational Isomers on Host-Guest Binding. J. Am. Chem. Soc. (1993), 115(3), 879-84.
• Luty, Brock A.; Wade, Rebecca C.; Madura, Jeffry D.; Davis, Malcolm E.; Briggs, James M.; McCammon, J. Andrew. Brownian Dynamics Simulations of Diffusional Encounters Between Triose Phosphate Isomerase and Glyceraldehyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate. J. Phys. Chem. (1993), 97(1), 233-7.
• Sikes, C. S.; Mueller, E.; Madura, J. D.; Drake, B. Polyamino acids as Antiscalants, Corrosion Inhibitors, and Dispersants: Atomic Force Microscopy and Mechanisms of Action. Proceedings for the National Association of Corrosion Engineers (1993).
• Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Computer Phys. Comm. (1991), 62, 187-197.
• Davis, M. E.; Madura, J. D.; Sines, J.; Luty, B.A.; Allison, S.A.; McCammen, J.A. Diffusion-Controlled Enzymatic Reactions. Methods in Enzymology (1991), 202.
• Hegde, Vidyadhar; Madhukar, Puttannachetty; Madura, Jeffry D.; Thummel, Randolph P. Fischer Route to pyrido[3,2-g]indoles. A Novel Receptor for Urea Derivatives. J. Am. Chem. Soc. (1990), 112(11), 4549-50.
• Madura, Jeffry D.; McCammon, J. Andrew. Department of Chemistry, Brownian Dynamics Simulation of Diffusional Encounters Between Triose Phosphate Isomerase and D-glyceraldehyde Phosphate. J. Phys. Chem. (1989), 93(21), 7285-7.
• Madura, J. D.; Pettitt, B. M.; Calef, D. Water under High Pressure. Mol. Phys. (1988), 64(2), 325-336.
• Madura, Jeffry D.; Pettitt, B. Montgomery. Effects of Truncating Long-Range Interactions in Aqueous Ionic Solution Simulations. Chem. Phys. Lett. (1988), 150(1-2), 105-8.
• Madura, Jeffry D.; Pettitt, B. Montgomery; McCammon, J. Andrew. Geometric Considerations in the Calculation of Relative Free Energies of Activation. Chem. Phys. Lett. (1987), 141(1-2), 83-7.
• Speedy, Robin J.; Madura, Jeffry D.; Jorgensen, William L. Network Topology in Simulated Water. J. Phys. Chem. (1987), 91(4), 909-13.
• Madura, Jeffry D.; Jorgensen, William L. Ab initio and Monte Carlo Calculations for a Nulcleophilic Addition Reaction in the Gas Phase and in Aqueous Solution. J. Am. Chem. Soc. (1986), 108(10), 2517-27.
• Jorgensen, W. L.; Chandrasekhar, J.; Buckner, J. K.; Madura, J. D. Computer Simulations of Organic Reactions in Solution. Ann. N. Y. Acad. Sci., (1986), 482, 198-209.
• Jorgensen, William L.; Madura, Jeffry D. Temperature and size dependence for Monte Carlo Simulations of TIP4P Water. Mol. Phys. (1985), 56(6), 1381-92.
• Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. Optimized Intermolecular Potential Functions for liquid Hydrocarbons. J. Amer. Chem. Soc. (1984), 106, 6638-6646.
• Houk, K.N.; Rondan, Nelson G.R.; Brown, Frank K.; Jorgensen, William L.; Madura, Jeffry D.; Spellmeyer, David C. Electronic Origins and Consequences of Pyramidalization of Asymmetric Alkenes in Ground and Triplet Excited States. J. Am. Chem. Soc. (1983), 105(19), 5980-8.
• Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. Impey, Roger W.; Klein, Michael L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. (1983), 79(2), 926-35.
• Jorgensen, William L.; Madura, Jeffry D. Solvation and Conformation of Methanol in Water. J. Am. Chem. Soc. (1983), 105(6), 1407-13.