Jeffry D. Madura - Publications

Chemistry and Biochemistry Duquesne University, Pittsburgh, PA, United States 
Physical Chemistry, Organic Chemistry

126 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE. A combined computational and experimental approach reveals the structure of a C/EBPβ:Spi-1 interaction required for gene transcription. The Journal of Biological Chemistry. PMID 30355733 DOI: 10.1074/Jbc.Ra118.005627  1
2018 Hong WC, Wasko MJ, Wilkinson DS, Hiranita T, Li L, Hayashi S, Snell DB, Madura JD, Surratt CK, Katz JL. Dopamine Transporter Dynamics of N-Substituted Benztropine Analogs with Atypical Behavioral Effects. The Journal of Pharmacology and Experimental Therapeutics. PMID 29945932 DOI: 10.1124/Jpet.118.250498  0.52
2017 Jean B, Surratt CK, Madura JD. Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes. Journal of Molecular Graphics & Modelling. 76: 143-151. PMID 28734204 DOI: 10.1016/J.Jmgm.2017.07.003  0.52
2017 Punihaole D, Jakubek RS, Workman RJ, Marbella LE, Campbell P, Madura JD, Asher SA. Monomeric Polyglutamine Structures that Evolve into Fibrils. The Journal of Physical Chemistry. B. PMID 28531354 DOI: 10.1021/Acs.Jpcb.7B04060  0.36
2016 Cai Z, Luck LA, Punihaole D, Madura JD, Asher SA. Photonic crystal protein hydrogel sensor materials enabled by conformationally induced volume phase transition. Chemical Science. 7: 4557-4562. PMID 30155102 DOI: 10.1039/C6Sc00682E  0.36
2016 Talbot JN, Geffert LM, Jorvig JE, Goldstein RI, Nielsen CL, Wolters NE, Amos ME, Munro CA, Dallman E, Mereu M, Tanda G, Katz JL, Indarte M, Madura JD, Choi H, et al. Rapid and sustained antidepressant properties of an NMDA antagonist/monoamine reuptake inhibitor identified via transporter-based virtual screening. Pharmacology, Biochemistry, and Behavior. PMID 27569602 DOI: 10.1016/J.Pbb.2016.08.007  1
2016 Berberich JA, Stouch TR, Manepalli S, Esposito EX, Madura JD. Biological Testing of Organophosphorus-Inactivated Acetylcholinesterase Oxime Reactivators Identified via Virtual Screening. Chemical Research in Toxicology. PMID 27494215 DOI: 10.1021/Acs.Chemrestox.6B00198  1
2016 Punihaole D, Workman RJ, Hong Z, Madura JD, Asher SA. Polyglutamine Fibrils: New Insights into Antiparallel β-sheet Conformational Preference and Side Chain Structure. The Journal of Physical Chemistry. B. PMID 26947327 DOI: 10.1021/Acs.Jpcb.5B11380  1
2016 Hong WC, Kopajtic TA, Xu L, Lomenzo SA, Jean B, Madura JD, Surratt CK, Trudell ML, Katz JL. 2-Substituted 3β-Aryltropane Cocaine Analogs Produce Atypical DAT Inhibitor Effects Without Inducing Inward-Facing DAT Conformations. The Journal of Pharmacology and Experimental Therapeutics. PMID 26769919 DOI: 10.1124/Jpet.115.230722  1
2016 Cai Z, Luck LA, Punihaole D, Madura JD, Asher SA. Photonic crystal protein hydrogel sensor materials enabled by conformationally induced volume phase transition Chemical Science. 7: 4557-4562. DOI: 10.1039/c6sc00682e  1
2015 Surratt CK, Madura JD. Editorial: In silico Modeling of Brain Receptors for Antidepressants, Psychostimulants, and Other CNS-Active Drugs. Frontiers in Pharmacology. 6: 302. PMID 26779020 DOI: 10.3389/Fphar.2015.00302  1
2015 Wasko MJ, Pellegrene KA, Madura JD, Surratt CK. A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets. Frontiers in Neurology. 6: 197. PMID 26441817 DOI: 10.3389/Fneur.2015.00197  1
2015 Gedeon PC, Thomas JR, Madura JD. Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter. Methods in Molecular Biology (Clifton, N.J.). 1215: 253-87. PMID 25330967 DOI: 10.1007/978-1-4939-1465-4_12  1
2015 Devlin KP, Glaid AJ, Brant JA, Zhang JH, Srnec MN, Clark DJ, Soo Kim Y, Jang JI, Daley KR, Moreau MA, Madura JD, Aitken JA. Polymorphism and second harmonic generation in a novel diamond-like semiconductor: Li2MnSnS4 Journal of Solid State Chemistry. 231: 256-266. DOI: 10.1016/J.Jssc.2015.08.011  1
2015 Ul-Haq Z, Madura JD. Preface Frontiers in Computational Chemistry. 1: vii-viii. DOI: 10.1016/B978-1-60805-865-5.50012-5  1
2015 Ul-Haq Z, Madura JD. Frontiers in Computational Chemistry Frontiers in Computational Chemistry. 1: 1-350.  1
2014 Nolan TL, Geffert LM, Kolber BJ, Madura JD, Surratt CK. Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter. Acs Chemical Neuroscience. 5: 784-92. PMID 25003748 DOI: 10.1021/Cn500133B  1
2014 Thomas JR, Gedeon PC, Madura JD. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins. 82: 2289-302. PMID 24753369 DOI: 10.1002/Prot.24588  1
2014 Pope D, Madura JD, Cascio M. β-Amyloid and neprilysin computational studies identify critical residues implicated in binding specificity. Journal of Chemical Information and Modeling. 54: 1157-65. PMID 24650257 DOI: 10.1021/Ci500015M  1
2014 Esposito EX, Stouch TR, Wymore T, Madura JD. Exploring the physicochemical properties of oxime-reactivation therapeutics for cyclosarin, sarin, tabun, and VX inactivated acetylcholinesterase. Chemical Research in Toxicology. 27: 99-110. PMID 24443939 DOI: 10.1021/Tx400350B  1
2014 Asciutto EK, Gaborek T, Madura JD. Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide Journal of Theoretical and Computational Chemistry. 13. DOI: 10.1142/S0219633614400045  1
2013 Immadisetty K, Madura JD. A review of monoamine transporter-ligand interactions. Current Computer-Aided Drug Design. 9: 556-68. PMID 24138394 DOI: 10.2174/15734099113096660039  1
2013 Gur M, Madura JD, Bahar I. Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophysical Journal. 105: 1643-52. PMID 24094405 DOI: 10.1016/J.Bpj.2013.07.058  1
2013 Immadisetty K, Geffert LM, Surratt CK, Madura JD. New design strategies for antidepressant drugs. Expert Opinion On Drug Discovery. 8: 1399-414. PMID 23991860 DOI: 10.1517/17460441.2013.830102  1
2012 Gaborek TJ, Chipot C, Madura JD. Conformational free-energy landscapes for a peptide in saline environments. Biophysical Journal. 103: 2513-20. PMID 23260053 DOI: 10.1016/J.Bpj.2012.11.001  1
2012 Merchant BA, Madura JD. Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. Journal of Molecular Graphics & Modelling. 38: 1-12. PMID 23079638 DOI: 10.1016/J.Jmgm.2012.05.007  1
2012 Manepalli S, Surratt CK, Madura JD, Nolan TL. Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective. The Aaps Journal. 14: 820-31. PMID 22918625 DOI: 10.1208/S12248-012-9391-0  1
2012 Thomas JR, Gedeon PC, Grant BJ, Madura JD. LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis. Biophysical Journal. 103: L1-3. PMID 22828348 DOI: 10.1016/J.Bpj.2012.05.002  1
2012 Asciutto EK, Young MJ, Madura J, Pochapsky SS, Pochapsky TC. Solution structural ensembles of substrate-free cytochrome P450(cam). Biochemistry. 51: 3383-93. PMID 22468842 DOI: 10.1021/Bi300007R  1
2011 Nolan TL, Lapinsky DJ, Talbot JN, Indarte M, Liu Y, Manepalli S, Geffert LM, Amos ME, Taylor PN, Madura JD, Surratt CK. Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization. Acs Chemical Neuroscience. 2: 544-552. PMID 21966587 DOI: 10.1021/Cn200044X  1
2011 Manepalli S, Geffert LM, Surratt CK, Madura JD. Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore. Journal of Chemical Information and Modeling. 51: 2417-26. PMID 21834587 DOI: 10.1021/Ci200280M  1
2011 Asciutto EK, Dang M, Pochapsky SS, Madura JD, Pochapsky TC. Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450cam. Biochemistry. 50: 1664-71. PMID 21265500 DOI: 10.1021/Bi101820D  1
2011 Jain P, Flaherty PT, Yi S, Chopra I, Bleasdell G, Lipay J, Ferandin Y, Meijer L, Madura JD. Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25. Bioorganic & Medicinal Chemistry. 19: 359-73. PMID 21144757 DOI: 10.1016/J.Bmc.2010.11.022  1
2011 Altun A, Bartlett RJ, Bergonzo C, Braun AR, Bylaska EJ, Daniel Crawford T, de Jong WA, Deumens E, Erik Nielsen J, Fortenberry RC, Govind N, Hayat S, Helms V, Jindal N, Johnston MA, ... ... Madura JD, et al. Contributors Annual Reports in Computational Chemistry. 7: ix-xi. DOI: 10.1016/B978-0-444-53835-2.00017-1  1
2011 Merchant BA, Madura JD. A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations Annual Reports in Computational Chemistry. 7: 67-87. DOI: 10.1016/B978-0-444-53835-2.00003-1  1
2011 Ziegler MJ, Madura JD. Solvation of metal cations in non-aqueous liquids Journal of Solution Chemistry. 40: 1383-1398. DOI: 10.1007/S10953-011-9732-0  1
2010 Hirst JD, Madura JD. Topical perspectives. Journal of Molecular Graphics & Modelling. 29: 115. PMID 20655257 DOI: 10.1016/j.jmgm.2010.07.001  1
2010 Hirst JD, Madura JD. The JMGM/MGMS graphics prize. Journal of Molecular Graphics & Modelling. 29: 1. PMID 20637669 DOI: 10.1016/J.Jmgm.2010.06.005  1
2010 Zaheer-ul-Haq, Halim SA, Uddin R, Madura JD. Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors. Journal of Molecular Graphics & Modelling. 28: 870-82. PMID 20447848 DOI: 10.1016/J.Jmgm.2010.03.007  1
2010 Indarte M, Liu Y, Madura JD, Surratt CK. Receptor-Based Discovery of a Plasmalemmal Monoamine Transporter Inhibitor via High Throughput Docking and Pharmacophore Modeling. Acs Chemical Neuroscience. 1: 223-233. PMID 20352074 DOI: 10.1021/Cn900032U  1
2010 Asciutto EK, General IJ, Xiong K, Xiong K, Asher SA, Madura JD. Sodium perchlorate effects on the helical stability of a mainly alanine peptide. Biophysical Journal. 98: 186-96. PMID 20338840 DOI: 10.1016/J.Bpj.2009.10.013  1
2010 Gedeon PC, Indarte M, Surratt CK, Madura JD. Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer. Proteins. 78: 797-811. PMID 19899168 DOI: 10.1002/Prot.22601  1
2010 Xiong K, Asciutto EK, Madura JD, Asher SA. Circular dichroism and UV resonance Raman study of the impact of salts and alcohols on the Gibbs free energy landscape of an α-helical peptide Aip Conference Proceedings. 1267: 858-859. DOI: 10.1063/1.3482854  1
2010 Asciutto EK, General IJ, Xiong K, Asher SA, Madura JD. Erratim: Sodium perchlorate effects on the helical stability of a mainly alanine peptide (Biophysical Journal (2010) 98 (186-196)) Biophysical Journal. 99: 2715. DOI: 10.1016/j.bpj.2010.09.035  1
2010 Dick TJ, Wierzbicki A, Madura JD. Free energy perturbation monte carlo simulations of salt influences on aqueous freezing point depression Practical Aspects of Computational Chemistry: Methods, Concepts and Applications. 359-370. DOI: 10.1007/978-90-481-2687-3_18  1
2010 Dick TJ, Wierzbicki A, Madura JD. CO2(aq) parameterization through free energy perturbation/monte carlo simulations for use in CO2 sequestration Practical Aspects of Computational Chemistry: Methods, Concepts and Applications. 337-357. DOI: 10.1007/978-90-481-2687-3_17  1
2009 Xiong K, Asciutto EK, Madura JD, Asher SA. Salt dependence of an alpha-helical peptide folding energy landscapes. Biochemistry. 48: 10818-26. PMID 19845367 DOI: 10.1021/Bi9014709  1
2009 Asciutto EK, Madura JD, Pochapsky SS, OuYang B, Pochapsky TC. Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam. Journal of Molecular Biology. 388: 801-14. PMID 19327368 DOI: 10.1016/J.Jmb.2009.03.046  1
2009 Hirst JD, Madura JD. Editorial Journal of Molecular Graphics and Modelling. 28: 1. DOI: 10.1016/j.jmgm.2009.07.003  1
2009 Cui J, Battle K, Wierzbicki A, Madura JD. Investigations of structure and dynamics of water solvation of the type I antifreeze protein International Journal of Quantum Chemistry. 109: 73-80. DOI: 10.1002/Qua.21857  1
2008 General IJ, Asciutto EK, Madura JD. Structure of aqueous sodium perchlorate solutions. The Journal of Physical Chemistry. B. 112: 15417-25. PMID 18991374 DOI: 10.1021/Jp806269W  1
2008 Snyder JA, Madura JD. Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study. The Journal of Physical Chemistry. B. 112: 7095-103. PMID 18476731 DOI: 10.1021/Jp7103769  1
2008 Zaheer-ul H, Uddin R, Yuan H, Petukhov PA, Choudhary MI, Madura JD. Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. Journal of Chemical Information and Modeling. 48: 1092-103. PMID 18444627 DOI: 10.1021/Ci8000056  1
2008 Asciutto EK, Mikhonin AV, Asher SA, Madura JD. Computational and experimental determination of the alpha-helix unfolding reaction coordinate. Biochemistry. 47: 2046-50. PMID 18189423 DOI: 10.1021/Bi702112V  1
2008 Indarte M, Madura JD, Surratt CK. Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template. Proteins. 70: 1033-46. PMID 17847094 DOI: 10.1002/Prot.21598  1
2008 Wierzbicki A, Knight CA, Salter EA, Henderson CN, Madura JD. Role of nonpolar amino acid functional groups in the surface orientation-dependent adsorption of natural and synthetic antifreeze peptides on ice Crystal Growth and Design. 8: 3420-3429. DOI: 10.1021/Cg8003855  1
2008 Esposito EX, Hopfinger AJ, Madura JD. 3D- and nD-QSAR Methods Handbook of Chemoinformatics. 4: 1575-1603. DOI: 10.1002/9783527618279.ch44e  1
2007 Zaheer-ul-Haq, Dalal P, Aronson NN, Madura JD. Family 18 chitolectins: comparison of MGP40 and HUMGP39. Biochemical and Biophysical Research Communications. 359: 221-6. PMID 17543889 DOI: 10.1016/J.Bbrc.2007.05.074  1
2007 Wierzbicki A, Dalal P, Cheatham TE, Knickelbein JE, Haymet AD, Madura JD. Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins. Biophysical Journal. 93: 1442-51. PMID 17526572 DOI: 10.1529/Biophysj.107.105189  1
2006 Zhou Z, Lin X, Madura JD. HIV-1 RT nonnucleoside inhibitors and their interaction with RT for antiviral drug development. Infectious Disorders Drug Targets. 6: 391-413. PMID 17168804 DOI: 10.2174/187152606779025833  1
2006 Zhou Z, Bates M, Madura JD. Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design. Proteins. 65: 580-92. PMID 16972282 DOI: 10.1002/Prot.21065  1
2006 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. 22: 179-85. PMID 16454509 DOI: 10.1021/Bp0501773  1
2006 Krouskop PE, Madura JD, Paschek D, Krukau A. Solubility of simple, nonpolar compounds in TIP4P-Ew. The Journal of Chemical Physics. 124: 16102. PMID 16409062 DOI: 10.1063/1.2138704  1
2006 Krouskop PE, Garrison J, Gedeon PC, Madura JD. A novel hybrid simulation for study of multiscale phenomena Molecular Simulation. 32: 825-830. DOI: 10.1080/08927020600779368  1
2006 Esposito EX, Tobi D, Madura JD. Comparative protein modeling Reviews in Computational Chemistry. 22: 57-167.  1
2005 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. Journal of the American Chemical Society. 127: 17253-60. PMID 16332074 DOI: 10.1021/Ja053973D  1
2005 Dalal P, Zanotti K, Wierzbicki A, Madura JD, Cheung HS. Molecular dynamics simulation studies of the effect of phosphocitrate on crystal-induced membranolysis. Biophysical Journal. 89: 2251-7. PMID 16040742 DOI: 10.1529/Biophysj.104.058503  1
2005 Dick TJ, Madura JD. Chapter 5 A Review of the TIP4P, TIP4P-Ew, TIP5P, and TIP5P-E Water Models Annual Reports in Computational Chemistry. 1: 59-74. DOI: 10.1016/S1574-1400(05)01005-4  1
2004 Zhou Z, Madura JD. CoMFA 3D-QSAR analysis of HIV-1 RT nonnucleoside inhibitors, TIBO derivatives based on docking conformation and alignment. Journal of Chemical Information and Computer Sciences. 44: 2167-78. PMID 15554687 DOI: 10.1021/Ci049893V  1
2004 Zhou Z, Madura JD. Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS. Proteins. 57: 493-503. PMID 15382241 DOI: 10.1002/Prot.20223  1
2004 Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics. 120: 9665-78. PMID 15267980 DOI: 10.1063/1.1683075  1
2004 Esposito EX, Hopfinger AJ, Madura JD. Methods for applying the quantitative structure-activity relationship paradigm. Methods in Molecular Biology (Clifton, N.J.). 275: 131-214. PMID 15141113 DOI: 10.1385/1-59259-802-1:131  1
2004 Krouskop PE, Madura JD. Studies of brine using TiP4P-EW and dynamo Acs National Meeting Book of Abstracts. 228.  1
2004 Thomas LL, Dick TJ, Madura JD. Investigation of natural gas clathrate hydrate formation and stability through Monte Carlo simulations Acs National Meeting Book of Abstracts. 227.  1
2003 Aronson NN, Halloran BA, Alexyev MF, Amable L, Madura JD, Pasupulati L, Worth C, Van Roey P. Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A. The Biochemical Journal. 376: 87-95. PMID 12932195 DOI: 10.1042/Bj20030273  1
2003 Zhou Z, Fisher D, Spidel J, Greenfield J, Patson B, Fazal A, Wigal C, Moe OA, Madura JD. Kinetic and docking studies of the interaction of quinones with the quinone reductase active site. Biochemistry. 42: 1985-94. PMID 12590585 DOI: 10.1021/Bi026518S  1
2003 Wierzbicki A, Dalal P, Madura JD, Cheung HS. Molecular dynamics simulation of crystal-induced membranolysis Journal of Physical Chemistry B. 107: 12346-12351. DOI: 10.1021/Jp0305988  1
2002 Zhou Z, Madrid M, Madura JD. Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase. Proteins. 49: 529-42. PMID 12402361 DOI: 10.1002/Prot.10233  1
2002 Carlier PR, Madura JD. Effective computational modeling of constitutional isomerism and aggregation states of explicit solvates of lithiated phenylacetonitrile. The Journal of Organic Chemistry. 67: 3832-40. PMID 12027700 DOI: 10.1021/Jo0255633  1
2002 Madura JD, Salter EA, Wierzbicki A, Dalal P, Harrington JP. Homology models for the tetrameric and dodecameric complexes of Lumbricus terrestris hemoglobin Journal of Molecular Structure: Theochem. 592: 173-181. DOI: 10.1016/S0166-1280(02)00238-5  1
2002 Lakshminarasimhulu P, Madura JD. A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape Computer Physics Communications. 144: 141-153. DOI: 10.1016/S0010-4655(02)00157-1  1
2002 Dick TJ, Acevedo O, Dalal P, Madura JD, Evanseck JD, Mathews JP. Molecular Basis for Carbon Dioxide Sequestration in Coal Acs Division of Fuel Chemistry, Preprints. 47: 14-16.  1
2001 Madrid M, Lukin JA, Madura JD, Ding J, Arnold E. Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding Proteins: Structure, Function and Genetics. 45: 176-182. PMID 11599020 DOI: 10.1002/Prot.1137  1
2001 Harris MN, Madura JD, Ming LJ, Harwood VJ. Kinetic and Mechanistic Studies of Prolyl Oligopeptidase from the Hyperthermophile Pyrococcus furiosus Journal of Biological Chemistry. 276: 19310-19317. PMID 11278687 DOI: 10.1074/Jbc.M010489200  1
2001 Dalal P, Knickelbein J, Haymet ADJ, Sönnichsen FD, Madura JD. Hydrogen bond analysis of Type 1 antifreeze protein in water and the ice/water interface Physchemcomm. 4: 1-5. DOI: 10.1039/B101331I  1
2001 Ravichandran S, Madura JD, 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. 105: 3610-3613. DOI: 10.1021/Jp010223R  1
2000 Esposito EX, Baran K, Kelly K, Madura JD. Docking of sulfonamides to carbonic anhydrase II and IV. Journal of Molecular Graphics & Modelling. 18: 283-9, 307-8. PMID 11021544 DOI: 10.1016/S1093-3263(00)00040-1  1
2000 Madura JD, Baran K, Wierzbicki A. Molecular recognition and binding of thermal hysteresis proteins to ice Journal of Molecular Recognition. 13: 101-113. PMID 10822254 DOI: 10.1002/(Sici)1099-1352(200003/04)13:2<101::Aid-Jmr493>3.0.Co;2-9  1
2000 Esposito EX, Baran K, Kelly K, Madura JD. Docking substrates to metalloenzymes Molecular Simulation. 24: 293-306. DOI: 10.1080/08927020008022377  1
2000 Spreitzer G, Whitling JM, Madura JD, Wright DW. Peptide-encapsulated CdS nanoclusters from a combinatorial ligand library Chemical Communications. 209-210.  1
1999 Madura JD. Using MOE to visualize molecular orbitals Journal of Molecular Graphics &Amp; Modelling. 17: 150-151. PMID 10680120  1
1999 Madura JD, Wierzbicki A. Chapter 14 Modeling of antifreeze proteins Theoretical and Computational Chemistry. 8: 537-568. DOI: 10.1016/S1380-7323(99)80089-2  1
1997 Wierzbicki A, Madura JD, Salmon C, Sönnichsen F. Modeling studies of binding of sea raven type II antifreeze protein to ice Journal of Chemical Information and Computer Sciences. 37: 1006-1010. PMID 9392856 DOI: 10.1021/Ci9702353  1
1997 Aronson NN, Blanchard CJ, Madura JD. Homology modeling of glycosyl hydrolase family 18 enzymes and proteins Journal of Chemical Information and Computer Sciences. 37: 999-1005. PMID 9392855 DOI: 10.1021/Ci970236V  1
1997 Madura JD, Lombardini JB, Briggs JM, Minor DL, Wierzbicki A. Physical and structural properties of taurine and taurine analogues Amino Acids. 13: 131-139. DOI: 10.1007/Bf01373211  1
1996 Wierzbicki A, Taylor MS, Knight CA, Madura JD, Harrington JP, Sikes CS. Analysis of shorthorn sculpin antifreeze protein stereospecific binding to (2-1 0) faces of ice. Biophysical Journal. 71: 8-18. PMID 8804585 DOI: 10.1016/S0006-3495(96)79204-4  1
1996 Wierzbicki A, Salter EA, Hoffman NW, Stevens ED, Van Do L, VanLoock MS, Madura JD. Structural investigations of trans-Rh(PY3)2(CO)X (X = F, Cl, NCO; Y = H, Me, Ph) using density functional theory and x-ray analysis Journal of Physical Chemistry. 100: 11250-11254. DOI: 10.1021/Jp952918W  1
1996 Davis JH, Madura JD. Synthesis and computational evaluation of a boronium ion analogue of the tropane ring system Tetrahedron Letters. 37: 2729-2730. DOI: 10.1016/0040-4039(96)00372-3  1
1996 Madura JD, Nakajima Y, Hamilton RM, Wierzbicki A, Warshel A. Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase Structural Chemistry. 7: 131-138. DOI: 10.1007/Bf02278738  1
1996 Madura JD, Taylor MS, Wierzbicki A, Harrington JP, Sikes CS, Sönnichsen F. The dynamics and binding of a Type III antifreeze protein in water and on ice Journal of Molecular Structure: Theochem. 388: 65-77.  1
1995 Wierzbicki A, Sikes CS, Sallis JD, Madura JD, Stevens ED, Martin KL. Scanning electron microscopy and molecular modeling of inhibition of calcium oxalate monohydrate crystal growth by citrate and phosphocitrate. Calcified Tissue International. 56: 297-304. PMID 7767841 DOI: 10.1007/Bf00318050  1
1995 Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program Computer Physics Communications. 91: 57-95. DOI: 10.1016/0010-4655(95)00043-F  1
1995 Schaffer SW, Azuma J, Madura JD. Mechanisms underlying taurine-mediated alterations in membrane function Amino Acids. 8: 231-246. DOI: 10.1007/Bf00806821  1
1995 Young SH, Madura JD, Wierzbicki A. Integration of numerical methods into the undergraduate physical chemistry curriculum using MATHCAD Journal of Chemical Education. 73: 609-610.  1
1994 Wierzbicki A, Sikes CS, Madura JD, Drake B. Atomic force microscopy and molecular modeling of protein and peptide binding to calcite Calcified Tissue International. 54: 133-141. PMID 8012868 DOI: 10.1007/Bf00296064  1
1994 Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA. Simulation of enzyme-substrate encounter with gated active sites. Nature Structural Biology. 1: 65-9. PMID 7656010 DOI: 10.1038/Nsb0194-65  1
1994 Madura JD, Wierzbicki A, Harrington JP, Maughon RH, Raymond JA, Sikes CS. Interactions of the D- and L-forms of winter flounder antifreeze peptide with the {201} planes of ice [25] Journal of the American Chemical Society. 116: 417-418. DOI: 10.1021/Ja00080A066  1
1994 Salter EA, Wierzbicki A, Seminario JM, Hoffman MW, Easterling ML, Madura JD. Structure of trans-Rh(PH3)2(CO)X (X = F, Cl) using Hartree-Fock/MBPT(2) and density functional theory Journal of Physical Chemistry. 98: 12945-12948.  1
1993 Wade RC, Davis ME, Luty BA, Madura JD, McCammon JA. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme Biophysical Journal. 64: 9-15. PMID 8431552 DOI: 10.1016/S0006-3495(93)81335-3  1
1993 Cannon WR, Madura JD, Thummel RP, McCammon JA. Molecular recognition: Effect of rotational isomers on host-guest binding Journal of the American Chemical Society. 115: 879-884.  1
1993 Luty BA, Wade RC, Madura JD, Davis ME, Briggs JM, McCammon JA. Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: Electrostatic steering of glyceraldehyde phosphate Journal of Physical Chemistry. 97: 233-237.  1
1991 Davis ME, Madura JD, Sines J, Luty BA, Allison SA, McCammon JA. Diffusion-controlled enzymatic reactions Methods in Enzymology. 202: 473-497. PMID 1784185 DOI: 10.1016/0076-6879(91)02024-4  1
1991 Davis ME, Madura JD, Luty BA, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program Computer Physics Communications. 62: 187-197. DOI: 10.1016/0010-4655(91)90094-2  1
1990 Hegde V, Madhukar P, Madura JD, Thummel RP. Fischer route to pyrido[3,2-g]indoles. A novel receptor for urea derivatives Journal of the American Chemical Society. 112: 4549-4550. DOI: 10.1021/Ja00167A066  1
1989 Madura JD, Pettitt BM, McCammon JA. Methods for calculating geometries of transition states in solution Chemical Physics. 129: 185-191. DOI: 10.1016/0301-0104(89)80003-5  1
1989 Madura JD, McCammon JA. Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phosphate Journal of Physical Chemistry. 93: 7285-7287.  1
1988 Madura JD, Pettitt BM, Calef DF. Water under high pressure Molecular Physics. 64: 325-336. DOI: 10.1080/00268978800100253  1
1988 Madura JD, Pettitt BM. Effects of truncating long-range interactions in aqueous ionic solution simulations Chemical Physics Letters. 150: 105-108. DOI: 10.1016/0009-2614(88)80404-4  1
1987 Madura JD, Pettitt BM, McCammon JA. Geometric considerations in the calculation of relative free energies of activation Chemical Physics Letters. 141: 83-87. DOI: 10.1016/0009-2614(87)80096-9  1
1987 Speedy RJ, Madura JD, Jorgensen WL. Network topology in simulated water Journal of Physical Chemistry. 91: 909-913.  1
1986 Jorgensen WL, Chandrasekhar J, Buckner JK, Madura JD. Computer simulations of organic reactions in solution. Annals of the New York Academy of Sciences. 482: 198-209. PMID 3471104 DOI: 10.1111/J.1749-6632.1986.Tb20951.X  1
1986 Madura JD, Jorgensen WL. Ab initio and monte carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solution Journal of the American Chemical Society®. 108: 2517-2527.  1
1985 Jorgensen WL, Madura JD. Temperature and size dependence for monte carlo simulations of TIP4P water Molecular Physics. 56: 1381-1392. DOI: 10.1080/00268978500103111  1
1984 Jorgensen WL, Madura JD, Swenson CJ. Optimized intermolecular potential functions for liquid hydrocarbons Journal of the American Chemical Society. 106: 6638-6646.  1
1983 Jorgensen WL, Madura JD. Solvation and conformation of methanol in water Journal of the American Chemical Society. 105: 1407-1413.  1
1983 Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics. 79: 926-935.  1
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