Publications

Articles (Refereed)

  1. Nolan, T. L., Geffert, L. M.; Kolber, B. J.; Madura, J. D.; Surratt, C. K. Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter. ACS Chemical Neuroscience (2014) 5, 784-792, DOI: 10.1021/cn500133b
  2. Thomas, James R. ; Gedeon, Patrick C.; Madura, Jeffry D. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins (2014) 82, 2289-2302, DOI: 10.1002/prot.24588
  3. Pope, D.; Madura, J. D.; Cascio, M. B-amyloid and neprilysin computational studies identify critical residues implicated in binding specificity. Chem. Inform. Modeling (2014) 54, 1157-1165.
  4. Esposito, E. X.; Stouch, T. R.; Wymore, T. Madura, J. D. Exploring the Physicochemical Properties of Oxime-Reactivation Therapeutics for Cyclosarin, Sarin, Tabun, and VX Inactivated Acetylcholinesterase. Res. Toxicol. (2014) 27, 99-110. DOI:10.1021/tx400350b
  5. Asciutto, E. K.; Gaborek, T.; Madura, J. D. Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide. Theo. Comp. Chem. (2014) 13.
  6. Gur, M.; Madura, J.D.; Bahar, I. Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase. J. (2013) 105 (7) 1643-1652. DOI: 10.1016/j.bpj.2013.07.058; PMID:24094405
  7. Immadisetty, K.; Geffert, L.M.; Surratt, C.K.; Madura, J.D. New design strategies for antidepressant drugs. Expert Opinion on Drug Discovery (2013), 8, 1399-1414. DOI:10.1517/17460441.2013.830102
  8. Immadisetty, K; Madura, J. D. A Review of Monoamine Transporter-Ligand Interactions. Current Computer-aided Drug Design (2013), 9, 556-568. PMID:24138394
  9. Gaborek, T. J.; Chipot, C.; Madura, J. D. Using multiple collective variables to examine salt effects on peptide conformational stability. J. (2012), 103, 2513-2520.
  10. Manepalli, Sankar; Surratt, C. K.; Madura, J. D.; Nolan, T. L. Monoamine Transporter Structure, Function, Dynamics, and Drug Discovery:A Computational Perspective. The AAPS Journal (2012), 14, p 820-831. DOI: 10.1208/s12248-012-9391-0
  11. Merchant, Bonnie A.; Madura, J. D. Insights from molecular dynamics: The binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. Mol. Graphics and Modeling (2012), 338, 1-12. DOI:10.1016/j.jmgm.2012.05.007
  12. Thomas, James; Gedeon, P.; Grant, B.; Madura, J. D. LeuT Conformational Sampling Utilizing Accelerated Molecular Dynamics and Principal Component Analysis. J. (2012), 103, p 1-3.
  13. Asciutto, E. K.; Young, M. J.; Madura, J; Pochapsky, S. S.; Pochapsky, T. C. Solution Structural Ensembles of Substrate-Free Cytochrome P450cam. Biochemistry (2012) 51, 3383-3393.
  14. Jain, Prashi; Flaherty, Patrick T.; Yi, Shuyan; Chopra, Ishveen; Bleasdell, Gwenyth; Lipay, Josh; Ferandin, Yoan; Meijer, Laurent; Madura, Jeffry D. Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25. Bioorganic & Medicinal Chemistry (2011), 19(1), 359-373. DOI:10.1016/j.bmc.2010.11.022
  15. Manepalli, Sankar; Geffert, Laura M.; Surratt, Christopher K.; Madura, Jeffry D. Discovery of Novel Selective Serotonin Reuptake Inhibitors through Development of a Protein-Based Pharmacophore. Journal of Chemical Information and Modeling (2011), 51(9), 2417-2426. DOI:10.1021/ci200280m
  16. Asciutto, Eliana K.; Dang, Marina; Pochapsky, Susan Sondej; Madura, Jeffry D.; Pochapsky, Thomas C. Experimentally Restrained Molecular Dynamics Simulations for Characterizing the Open States of Cytochrome P450cam. Biochemistry (2011), 50(10), 1664-1671. DOI:10.1021/bi101820d
  17. Nolan, Tammy L.; Lapinsky, David J.; Talbot, Jeffery N.; Indarte, Martin; Liu, Yi; Manepalli, Sankar; Geffert, Laura M.; Amos, Mary Ellen; Taylor, Phillip N.; Madura, Jeffry D.; Surratt, Christopher, K. Identification of a Novel Selective Serotonin Reuptake Inhibitor by Coupling Monoamine Transporter-Based Virtual Screening and Rational Molecular Hybridization. ACS Chemical Neuroscience (2011), 2(9), 544-552. DOI:10.1021/cn200044x
  18. Ziegler, Michael J.; Madura, Jeffry D. Solvation of Metal Cations in Non-aqueous Liquids. Journal of Solution Chemistry (2011), 40(8), 1383-1398. DOI:10.1007/s10953-011-9732-0
  19. Kuhel J. J., Wheeler M. C., Miele P. E., Holder D. A., Johnson B., Paterno Parsi A. A., Madura J. D. Quantitative Impact of an Artificial Intelligence Tutoring System on Student Performance in Assigning Oxidation Numbers in Chemical Formulas. Educator (2010), 15, 455-460.
  20. Zaheer-ul-Haq; Halim, Sobia Ahsan; Uddin, Reaz; Madura, Jeffry D. Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors. Journal of Molecular Graphics & Modeling (2010), 28(8), 870-882.
  21. Indarte, M., Liu, Y., Madura, J.D., Surratt. C.K., Receptor-Based Discovery of a Plasmalemmal Monoamine Transporter Inhibitor via High-Throughput Docking and Pharmacophore. ACS Chemical Neuroscience (2010), 1(3), 223-233.
  22. Asciutto, Eliana K. General, Ignacio J. Xiong, Kan; Asher, Sanford; Madura, Jeffry. D. Sodium perchlorate effects on the helical stability of a mainly alanine peptide. J. (2010), 98(2), 186-196.
  23. Gedeon, P. G.; Indarte, M; Surratt, C. K.; Madura, J. D. Molecular Dynamics of Leucine and Dopamine Transporter Proteins in a Model Cell Membrane Lipid Bilayer. Proteins: Structure, Function and Bioinformatics (2010), 78(4), 797-811.
  24. Kan Xiong, Eliana K. Asciutto, Jeffry D. Madura and Sanford A Asher. Salt Dependence of -helical Peptide Folding Energy Landscapes. Biochemistry (2009), 48, 10818-10826.
  25. Asciutto, Eliana K.; Madura, Jeffry D.; Pochapsky, Susan Sondej; OuYang, Bo; Pochapsky, Thomas C. Structural and Dynamic Implications of an Effector-induced Backbone Amide cis-trans Isomerization in Cytochrome P450cam. Mol. Biol. (2009) 388, 801-814.
  26. Asciutto, Eliana K.; Mikhonin, Aleksandr V.; Asher, Sanford A.; Madura, Jeffry, D. Computational and Experimental Determination of the $\alpha$-Helix Unfolding Reaction Coordinate. Biochemistry (2008), 47(7), 2046-2050. DOI:10.1021/bi702112v
  27. Snyder, James A.; Madura, Jeffry, D. Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study. Journal of Physical Chemistry B (2008), 112(23), 7095-7103. DOI:10.1021/jp7103769
  28. Cui, Jun; Battle, Keith; Wierzbicki, Andrzej; Madura, Jeffry, D. Investigations of structure and dynamics of water solvation of the type I antifreeze protein. International Journal of Quantum Chemistry (2008), 109(1), 73-80. DOI: 10.1002/qua.21857
  29. Zaheer-ul-Haq; Uddin, Reaz; Yuan, Hongbin; Petukhov, Pavel A.; Choudhary, M. Iqbal; Madura, Jeffry, D. Receptor-Based Modeling and 3D-QSAR for a Quantitative Production of the Butyrylcholinesterase Inhibitors Based on Genetic Algorithm. Journal of Chemical Information and Modeling (2008), 48(5), 1092-1103. DOI:10.1021/ci8000056
  30. Wierzbicki, Andrzej; Knight, Charles A.; Salter, E. Alan; Henderson, Camden N.; Madura, Jeffry, D. Role of Nonpolar Amino Acid Functional Groups in the Surface Orientation-Dependent Adsorption of Natural and Synthetic Antifreeze Peptides on Ice. Crystal Growth & Design (2008), 8(9), 3420-3429. DOI: 10.1021/cg8003855
  31. General, Ignacio J.; Asciutto, Eliana K.; Madura, Jeffry, D. Structure of Aqueous Sodium Perchlorate Solutions. Journal of Physical Chemistry B (2008), 112(48), 15417-15425. DOI: 10.1021/jp806269w
  32. Indarte, Martin; Madura, Jeffry D.; Surratt, Christopher K. Dopamine transporter comparative molecular modeling and binding site prediction using the LeuTAa leucine transporter as a template. Proteins: Structure, Function, and Bioinformatics (2008) 70(3), 1033-1046. DOI: 10.1002/prot.21598
  33. Wierzbicki, Andrzej; Dalal, Pranav; Cheatham, Thomas E., III; Knickelbein, Jared E.; Haymet, A. D. J.; Madura, Jeffry, D. Antifreeze proteins at the ice/water interface: Three calculated discriminating properties for orientation of type I proteins. Biophysical Journal (2007), 93(5), 1442-1451. DOI:10.1529/biophysj.107.105189
  34. ul-Haq, Z.; Dalal, P.; Aronson, Jr., N. N.; Madura, J. D. Family 18 chitolectins: Comparison of MGP40 and HUMGP39. Biophys. Res. Commun. (2007), 359(2), 221-226. DOI:10.1016/j.bbrc.2007.05.074
  35. Zhou, Z., Lin, X., Madura, J. D. HIV-1 RT nonnucleoside inhibitors and their interaction with RT for antivirtal drug development. Infectious Disorders: Drug Targets (2006) 6(4), 391-413.
  36. Zhou, Z.; Bates, M.; Madura, J. D. Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design. Proteins (2006) 65(3), 580-592. DOI: 10.1002/prot.21065
  37. Krouskop, P. E.; Garrison, P. C.; Gedeon, P. C.; Madura, J. D. A novel hybrid simulation for study of multiscale phenomena. Sim. (2006) 32(10-11), 825-830. DOI: 10.1080/08927020600779368
  38. Krouskop, P; Madura, JD; Paschek, D; Krukau, A. Solubility of simple, nonpolar compounds in TIP4P-Ew. Journal of Chemical Physics (2006) 124(1), 016102/1-06102/2. DOI: 10.1063/1.2138704
  39. Esposito, Emilio Xavier; Tobi, Dror; Madura, Jeffry D. Comparative protein modeling. Reviews in Computational Chemistry (2006), 22, 57-167.
  40. Munshi, R; Coalson, RD; Ermentrout, GB; Madura, JD; Meirovitch, H; Stiles, JR; Bahar, I. An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research. Biotechnology Progress (2006) 22(1), 179-185. DOI: 10.1021/bp0501773
  41. Zhou Z; Madrid M; Evanseck JD; Madura JD. Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 Reverse Transcriptase. Amer. Chem. Soc. (2005) 127:17253-17260. DOI: 10.1021/ja053973d
  42. Dalal, P; Zanotti, K; Wierzbicki, A; Madura, JD; Cheung, HS. Molecular dynamics simulation studies of the effect of phosphocitrate on crystal-induced membranolysis. Biophysical J. (2005) 89(4) 2251-2257. DOI: 10.1529/biophysj.104.058503
  43. 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. DOI:10.1016/j.actbio.2004.11.006
  44. 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. DOI: 10.1002/prot.20223..
  45. 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.
  46. 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. DOI: 10.1063/1.1683075
  47. Zhou, Z.; Madura, J. D. CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment. Chem. Infor. Comput. Sci. (2004), 44, 2167-2178. DOI: 10.1021/ci049893v.
  48. 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.
  49. 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. DOI: 10.1042/BJ20030273
  50. Wierzbicki, A.; Dalal, P.; Madura, J.D. Molecular Dynamics Simulations of Crystal Induced Membranolysis. Phys. Chem. B (2003), 107, 12345-12351. DOI: 10.1021/jp0305988
  51. 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. DOI: 10.1021/bi026518s
  52. 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. DOI:10.1016/S0166-1280(02)00238-5
  53. 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. DOI: 10.1333/s00897020620a
  54. 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. DOI: 10.1002/prot.10233
  55. 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. DOI: 10.1021/jo0255633
  56. 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.
  57. 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. DOI: 10.1016/S0010-4655(02)00157-1
  58. Esposito, Emilio Xavier; Baran, Kelli; Kelly, Ken; Madura, Jeffry D. Docking Substrates To Metalloenzymes. Molecular Simulation (2001), 24(4-6), 293-306.
  59. 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. DOI: 10.1002/prot.1137
  60. 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. DOI: 10.1039/b101331i
  61. 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. DOI: 10.1074/jbc.M010489200
  62. 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. DOI: 10.1021/jp010223r
  63. 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. DOI: 10.1039/a907178d
  64. Esposito, E.X.; Baran, K.; Kelly, K.; Madura, J.D. Docking of Sulfonamides To Carbonic Anhydrase II and IV. Journal of Molecular Graphics & Modeling (2000), 18(3), 283-289. DOI: 10.1016/S1093-3263(00)00040-1
  65. 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. DOI: 10.1002/(SICI)1099-1352(200003/04)13:2.
  66. 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. DOI: 10.1007/BF01373211
  67. 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. DOI: 10.1021/ci970236v
  68. 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. DOI: 10.1021/ci9702353
  69. 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. DOI: 10.1016/S0006-3495(96)79204-4
  70. 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. DOI: 10.1021/jp952918w
  71. 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. Toxicol. and Chem. (1996), 15(6), 824-836. DOI:10.1897/1551-5028(1996)015<0824:GFEOFO>2.3.CO;2
  72. 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. Chem. (1996), 7(2), 131-138. DOI: 10.1007/BF02278738
  73. 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. DOI:10.1016/0040-4039(96)00372-3
  74. 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. DOI:10.1016/S0166-1280(96)80020-0
  75. 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. Phys. Commun. (1995), 91-(1-3), 57-95 DOI: 10.1016/S0166-1280(96)80020-0
  76. 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. DOI: 10.1002/jcc.540160904
  77. Young, Sidney, H.; Madura, Jeffry D.; Wierzbicki, Andrzej. Integration of Numerical Methods Into The Undergraduate Physical Chemistry Curriculum Using MATHCAD. Chem. Educ. (1995), 72(7), 609-10.
  78. Schaffer, S. W.; Azuma, J.; Madura, J.D. Mechanisms Underlying Taurine-Mediated Alterations In Membrane Function.   Amino Acids (1995), 8(3), 231-46. DOI: 10.1007/BF00806821
  79. 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. DOI: 10.1007/BF00318050
  80. 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. DOI:10.1007/BF00296064
  81. 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.   Amer. Chem. Soc. (1994), 116, 417-418. DOI: 10.1021/ja00080a066
  82. 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.   Phys. Chem. (1994), 98, 12945-12948. DOI: 10.1021/j100100a022
  83. 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.   Nature Struct. Biol. (1994), 1(1), 65-9. DOI:10.1038/nsb0194-65
  84. 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.   J. (1993), 64(1), 9-15. DOI:10.1016/S0006-3495(93)81335-3
  85. Cannon, William R.; Madura, Jeffry D.; Thummel, Randolph P.; McCammon, J. Andrew. Molecular Recognition: Effect of Rotational Isomers on Host-Guest Binding.   Am. Chem. Soc.(1993), 115(3), 879-84. DOI: 10.1021/ja00056a009
  86. 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.   Phys. Chem. (1993), 97(1), 233-7. DOI: 10.1021/j100103a040
  87. 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).
  88. 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. DOI:10.1016/0010-4655(91)90094-2
  89. 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. 473-79. DOI:10.1016/0076-6879(91)02024-4
  90. Hegde, Vidyadhar; Madhukar, Puttannachetty; Madura, Jeffry D.; Thummel, Randolph P. Fischer Route to pyrido[3,2-g]indoles. A Novel Receptor for Urea Derivatives. Am. Chem. Soc.(1990), 112(11), 4549-50. DOI: 10.1021/ja00167a066
  91. Madura, Jeffry D.; McCammon, J. Andrew. Department of Chemistry, Brownian Dynamics Simulation of Diffusional Encounters Between Triose Phosphate Isomerase and D-glyceraldehyde Phosphate. Phys. Chem. (1989), 93(21), 7285-7. DOI: 10.1021/j100358a002
  92. Madura, J. D.; Pettitt, B. M.; Calef, D. Water under High Pressure. Phys. (1988), 64(2), 325-336. DOI: 10.1080/00268978800100253
  93. Madura, Jeffry D.; Pettitt, B. Montgomery. Effects of Truncating Long-Range Interactions in Aqueous Ionic Solution Simulations. Phys. Lett.(1988), 150(1-2), 105-8. DOI:10.1016/0009-2614(88)80404-4
  94. Madura, Jeffry D.; Pettitt, B. Montgomery; McCammon, J. Andrew. Geometric Considerations in the Calculation of Relative Free Energies of Activation. Phys. Lett. (1987), 141(1-2), 83-7. DOI: 10.1016/0009-2614(87)80096-9
  95. Speedy, Robin J.; Madura, Jeffry D.; Jorgensen, William L. Network Topology in Simulated Water. Phys. Chem. (1987), 91(4), 909-13. DOI: 10.1021/j100288a029
  96. 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. Am. Chem. Soc. (1986), 108(10), 2517-27. DOI: 10.1021/ja00270a005
  97. Jorgensen, W. L.; Chandrasekhar, J.; Buckner, J. K.; Madura, J. D. Computer Simulations of Organic Reactions in Solution. N. Y. Acad. Sci. (1986), 482, 198-209. DOI: 10.1111/j.1749-6632.1986.tb20951.x
  98. Jorgensen, William L.; Madura, Jeffry D. Temperature and size dependence for Monte Carlo Simulations of TIP4P Water. Phys. (1985), 56(6), 1381-92. DOI: 10.1080/00268978500103111
  99. Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. Optimized Intermolecular Potential Functions for liquid Hydrocarbons. Amer. Chem. Soc. (1984), 106, 6638-6646. DOI: 10.1021/ja00334a030
  100. 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. Am. Chem. Soc. (1983), 105(19), 5980-8. DOI: 10.1021/ ja00357a004
  101. Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. Impey, Roger W.; Klein, Michael L. Comparison of Simple Potential Functions for Simulating Liquid Water. Chem. Phys.(1983), 79(2), 926-35. DOI:10.1063/1.445869
  102. Jorgensen, William L.; Madura, Jeffry D. Solvation and Conformation of Methanol in Water. Am. Chem. Soc. (1983), 105(6), 1407-13. DOI: 10.1021/ja00344a001

Books

  1. Bissonette, Herring, and Madura General Chemistry, 11th edition, 2013 (co-author)
  2. Petrucci, Bissonette, Herring, and Madura General Chemistry, 10th edition, 2010 (co-author)
  3. Waldeck and Madura Solutions Manual for Physical Chemistry, 2009.
  4. Metiu Physical Chemistry volumes 1-4, 2006 (author of the Mathcad documents on accompanying CD-ROM)
  5. Petrucci, Harwood, Herring, and Madura General Chemistry, 9th edition, 2006 (co-author)

Book Chapters

  1. Gedeon, P. C.; Thomas, J. R.; and Madura, J. D. Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter Molecular Modeling of Proteins, Methods in Molecular Biology, vol. 1215,(2014) DOI 10.1007/978-1-4939-1465-4_12
  2. Merchant, B. A; Madura, J. D. A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations Annual Reports in Computational Chemistry (2011), 7, 68-84.
  3. Madura, J. D.; Wierzbicki, A.; Cui, J. and Battle, K. Antifreeze Proteins: A computational perspective from the past 10 years., Biochemistry and Function of Antifreeze Proteins, Stefan P. Gaether, editor (2010).
  4. Dick, T. J., Wierzbicki, A., Madura, J. D. CO2(aq) Parameterization through FEP/MC Simulations for use in CO2 Sequestration (2009) in Practical Aspects of Computational Chemistry, Chapter 17.
  5. Dick, T. J., Wierzbicki, A., Madura, J. D. CO2(aq) Calculation of Salt Influences on Aqueous Freezing Point Depression (2009) in Practical Aspects of Computational Chemistry, Chapter 18.
  6. Esposito EX, Tobi D, Madura JD. Comparative Protein Modeling. Reviews in Computational Chemistry (2005), 22, 57-167.
  7. Dick, Thomas J.; Madura, Jeffry D. A Review of TIP4P: TIP4P-Ew, TIP5P and TIP5P-E Water Models Annual Reports in Computational Chemistry (2005), 1, 59-74.
  8. Esposito, Emilio X; Hopfinger, Anton J; Madura, Jeffry D. Methods for Applying the Quantitative Structure-Activity Relationship Paradigm. Methods in Molecular Biology (2004), 275 (Cheminformatics), 131-213.
  9. Madura, Jeffry D; Wierzbicki, Andrzej. Molecular Modeling of Adsorption at Crystal Surfaces and Interfaces, in From Fluid-Solid Interfaces to Nanostructural Engineering; Eds.: DeYoreo, Jim; Liu, Xiang Yang, (2004), 2, 1-53.
  10. Esposito, Emilio X.; Hopfinger, Anton J.; Madura, Jeffry D. 3D- and nD-QSAR Methods, in Chemoinformatics- From Data to Knowledge, Volume II: Advanced Topics; Johann Gasteiger and Thomal Engel, Eds.: Wiley-VCH: Germany, (2003) 4, 1576-1603.
  11. Madura, Jeffry D.; Wierzbicki, Andrzej. Modeling of antifreeze proteins. Theoretical and Computational Chemistry (1999), 8(Computational Molecular Biology), 537-568.
  12. Young, Sidney, H.; Madura, Jeffry D.; Rioux, Frank. Department of Chemistry, University of South Alabama, Mobile, AL, USA. Software for Teaching and Using Numerical Methods In Physical Chemistry. Editor(s): Zielinski, Theresa Julia; Swift, Mary L. Using Computers in Chemistry and Chemical Education (1997), 163-185. Publisher: American Chemical Society, Washington, D.C.
  13. Madura, Jeffry D.; Davis, Malcolm E.; Gilson, Michael K.; Wade, Rebecca C.; Luty, Brock A.; McCammon, J. Andrew. Department of Chemistry, University of South Alabama, Mobile, AL, USA. Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations. Comput. Chem. (1994), 5 229-67.
  14. DeKock, Roger L.; Madura, Jeffry D.; Rioux, Frank; Cassanova, Joseph. Dept. Chem., Calvin College, Grand Rapids, MI, USA. Computational Chemistry in the Undergraduate Curriculum. Comput. Chem. (1993), 4 149-228.
  15. Davis, Malcolm E.; Madura, Jeffry D.; Sines, Jacqueline; Luty, Brock A.; Allison, Stuart A.; McCammon, J. Andrew. Diffusion-controlled enzyme reactions. Methods Enzymol. (1991) 202( Des. Model: Concepts Appl., Pt A), 473-97.
  16. Jorgensen, William L.; Blake, James F.; Madura, Jeffry D.; Wierschke, Scott D. Computer simulations of organic reactions in solution. ACS Symp. Ser. (1987) 353( Res. Chem. Chem. Eng.), 200-17.

Articles (Non-Refereed)

  1. Madura, Jeffry D. Chemistry entry for Scribner Dictionary of American History. (2003).
  2. Stouch, Terry R.; Brooks, Bernard R.; Swope, William C.; Madura, Jeffry D.; Halgren, Thomas A.; Houk, Kendall N.; McKelvey, John; Jorgensen, William L.; Lipkowitz, Kenny B.; Boyd, Donald B. A Letter to the Community of Computational Chemists-The Gordon Research Conferences on Computational Chemistry. Mol. Graphics Modelling (2001), 19(6), 617.
  3. Madura, Jeffry D. Using MOE to Visualize Molecular Orbitals. Journal of Molecular Graphics and Modeling (1999), 17(2), 150-1.
  4. Madura, Jeffry D. Computational Chemistry on a Shoestring: Software from QCPE. Council on Undergraduate Research Quarterly. (1995), 155-157.
  5. Madura, Jeffry D. MOBY 1.5. J. Chem. Inf. Comput. Sci. (1993).
  6. Madura, Jeffry D. Brownian Dynamics Simulations. Tech. Conf.- Soc. Plast. Eng. (1992), 50th(2), 2274-6.
  7. Madura, Jeffry D. Software Review of Dimensional Reasoner. Computers Chem. (1992), 16(4), 347.
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