| 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 |
0.75 |
|
| 2017 |
Galbraith ML, Madura JD. Identifying trends in hydration behavior for modifications to the hydrophobicity of poly(n-isopropylacrylamide). Journal of Molecular Graphics & Modelling. 78: 168-175. PMID 29073554 DOI: 10.1016/J.Jmgm.2017.09.021 |
0.303 |
|
| 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 |
0.314 |
|
| 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 |
0.783 |
|
| 2017 |
Srnec MN, Upadhyay S, Madura JD. A Python Program for Solving Schrödinger’s Equation in Undergraduate Physical Chemistry Journal of Chemical Education. 94: 813-815. DOI: 10.1021/Acs.Jchemed.7B00003 |
0.747 |
|
| 2017 |
Benner EM, Madura JD. Computational Investigation of the Serotonin Transporter Conformation and Reset Mechanism Biophysical Journal. 112: 128a. DOI: 10.1016/J.Bpj.2016.11.712 |
0.324 |
|
| 2017 |
Workman RJ, Punihaole D, Jakubek RS, Madura JD. Characterization of the Conformational Ensemble of Polyglutamine Peptides via Metadynamics MD Simulations and UV Resonance Raman Spectroscopy Biophysical Journal. 112: 470a. DOI: 10.1016/J.Bpj.2016.11.2520 |
0.766 |
|
| 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 |
0.756 |
|
| 2016 |
Asciutto EK, Gedeon PC, General IJ, Madura JD. Structure and Dynamics Study of LeuT Using Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States. The Journal of Physical Chemistry. B. PMID 27311999 DOI: 10.1021/Acs.Jpcb.6B02053 |
0.755 |
|
| 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 |
0.774 |
|
| 2016 |
Benner EM, Madura JD. Computational Investigation of the Transport Mechanism of Neurotransmitter Sodium Symporters using a Physiological Ion Gradient Biophysical Journal. 110: 626a. DOI: 10.1016/J.Bpj.2015.11.3355 |
0.305 |
|
| 2016 |
Workman RJ, Madura JD. Evaluating Free Energies of Dimerization of Short Polyglutamine Peptides with Molecular Dynamics Simulations Biophysical Journal. 110: 400a. DOI: 10.1016/J.Bpj.2015.11.2161 |
0.789 |
|
| 2016 |
Cascio M, Veeramachaneni RJ, Madura J. Human α1 Glycine Receptor Allostery as Identified by State-Dependent Crosslinking Studies Biophysical Journal. 110: 201a. DOI: 10.1016/J.Bpj.2015.11.1124 |
0.319 |
|
| 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 |
0.371 |
|
| 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 |
0.767 |
|
| 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 |
0.379 |
|
| 2015 |
Workman RJ, Madura JD. Evaluating Polyglutamine Peptide Monomers and Dimers with Enhanced Sampling MD Simulations Biophysical Journal. 108: 468a. DOI: 10.1016/J.Bpj.2014.11.2558 |
0.786 |
|
| 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 |
0.357 |
|
| 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 |
0.377 |
|
| 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 |
0.331 |
|
| 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 |
0.724 |
|
| 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 |
0.358 |
|
| 2014 |
Workman RJ, Madura JD. Assessing Polyglutamine Conformation and Aggregation with Molecular Dynamics Techniques Biophysical Journal. 106: 57a. DOI: 10.1016/J.Bpj.2013.11.393 |
0.783 |
|
| 2014 |
Thomas JR, Gedeon PC, Madura JD. Analyzing a Conformational Sampling of LeuT from Accelerated Molecular Dynamics Simulations Biophysical Journal. 106: 364a. DOI: 10.1016/J.Bpj.2013.11.2067 |
0.374 |
|
| 2014 |
Benner E, Acevedo MJ, Madura JD. Assessing the Transport Mechanism of Neurotransmitter Sodium Symporter Proteins with Molecular Dynamics Biophysical Journal. 106: 255a-256a. DOI: 10.1016/J.Bpj.2013.11.1501 |
0.314 |
|
| 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 |
0.326 |
|
| 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 |
0.323 |
|
| 2013 |
Workman RJ, Madura JD. The Conformational Energy Landscape of Aqueous Polyglutamine Peptides from Metadynamics Calculations Biophysical Journal. 104: 170a. DOI: 10.1016/J.Bpj.2012.11.958 |
0.781 |
|
| 2013 |
Gur M, Madura J, Bahar I. Global Transitions or Proteins Explored by a Multiscale Hybrid Methodology: Application to Dopamine Transporter Biophysical Journal. 104: 226a-227a. DOI: 10.1016/J.Bpj.2012.11.1279 |
0.346 |
|
| 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 |
0.378 |
|
| 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 |
0.312 |
|
| 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 |
0.787 |
|
| 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 |
0.364 |
|
| 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 |
0.327 |
|
| 2012 |
Merchant BA, Madura JD. Dynamics of the Dopamine Transporter in Various States in the Presence of an Explicit Sodium Gradient Biophysical Journal. 102: 660a. DOI: 10.1016/J.Bpj.2011.11.3597 |
0.306 |
|
| 2012 |
Gaborek TJ, Madura JD. Salt Effects on the Conformational Stability of Small Peptides Biophysical Journal. 102: 44a. DOI: 10.1016/J.Bpj.2011.11.272 |
0.366 |
|
| 2012 |
Gur M, Madura J, Bahar I. Transition Pathways of Proteins Explored by Combining Molecular Dynamics Simulations and Monte Carlo Sampling of Collective Modes Biophysical Journal. 102: 450a. DOI: 10.1016/J.Bpj.2011.11.2467 |
0.345 |
|
| 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 |
0.773 |
|
| 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 |
0.775 |
|
| 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 |
0.367 |
|
| 2011 |
Gaborek TJ, Madura JD, Merchant BA. Computational Investigation of the Effect of Ions on the Secondary Structure of Small Peptides Biophysical Journal. 100: 378a. DOI: 10.1016/J.Bpj.2010.12.2251 |
0.331 |
|
| 2011 |
Merchant BA, Madura JD. Ligand Exit and Entry Pathways for Monoamine Transporters Biophysical Journal. 100: 245a. DOI: 10.1016/J.Bpj.2010.12.1554 |
0.316 |
|
| 2011 |
Asciutto EK, Madura JD. Effects of Potassium and Sodium Ions on the Stability of Poly-L-Glutamate Biophysical Journal. 100: 209a. DOI: 10.1016/J.Bpj.2010.12.1350 |
0.336 |
|
| 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 |
0.308 |
|
| 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 |
0.303 |
|
| 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 |
0.331 |
|
| 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 |
0.751 |
|
| 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 |
0.333 |
|
| 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 |
0.306 |
|
| 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 |
0.359 |
|
| 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 |
0.314 |
|
| 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 |
0.753 |
|
| 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 |
0.341 |
|
| 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 |
0.311 |
|
| 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 |
0.348 |
|
| 2008 |
Esposito EX, Hopfinger AJ, Madura JD. 3D- and nD-QSAR Methods Handbook of Chemoinformatics. 4: 1575-1603. DOI: 10.1002/9783527618279.ch44e |
0.722 |
|
| 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 |
0.311 |
|
| 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 |
0.363 |
|
| 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 |
0.686 |
|
| 2006 |
Esposito EX, Tobi D, Madura JD. Comparative protein modeling Reviews in Computational Chemistry. 22: 57-167. |
0.684 |
|
| 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 |
0.637 |
|
| 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 |
0.304 |
|
| 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 |
0.306 |
|
| 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 |
0.343 |
|
| 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 |
0.337 |
|
| 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 |
0.311 |
|
| 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 |
0.777 |
|
| 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 |
0.305 |
|
| 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 |
0.331 |
|
| 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 |
0.317 |
|
| 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 |
0.308 |
|
| 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 |
0.303 |
|
| 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. |
0.686 |
|
| 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 |
0.311 |
|
| 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 |
0.733 |
|
| 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 |
0.309 |
|
| 2000 |
Esposito EX, Baran K, Kelly K, Madura JD. Docking substrates to metalloenzymes Molecular Simulation. 24: 293-306. DOI: 10.1080/08927020008022377 |
0.693 |
|
| 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 |
0.576 |
|
| 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 |
0.311 |
|
| 1996 |
Madura JD, Taylor MS, Wierzbicki A, Harrington JP, Sikes C, 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. DOI: 10.1016/S0166-1280(96)80020-0 |
0.322 |
|
| 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 |
0.343 |
|
| 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 |
0.64 |
|
| 1995 |
Gilson MK, McCammon JA, Madura JD. Molecular dynamics simulation with a continuum electrostatic model of the solvent Journal of Computational Chemistry. 16: 1081-1095. DOI: 10.1002/Jcc.540160904 |
0.643 |
|
| 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 |
0.335 |
|
| 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 |
0.709 |
|
| 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 |
0.609 |
|
| 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. DOI: 10.1021/Ja00056A009 |
0.704 |
|
| 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 The Journal of Physical Chemistry. 97: 233-237. DOI: 10.1021/J100103A040 |
0.709 |
|
| 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. |
0.513 |
|
| 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 |
0.463 |
|
| 1989 |
Madura JD, McCammon JA. Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phosphate The Journal of Physical Chemistry. 93: 7285-7287. DOI: 10.1021/J100358A002 |
0.443 |
|
| 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 |
0.545 |
|
| 1988 |
Madura JD, Pettitt BM, Calef DF. Water under high pressure Molecular Physics. 64: 325-336. DOI: 10.1080/00268978800100253 |
0.503 |
|
| 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 |
0.528 |
|
| 1987 |
Speedy RJ, Madura JD, Jorgensen WL. Network topology in simulated water The Journal of Physical Chemistry. 91: 909-913. DOI: 10.1021/J100288A029 |
0.449 |
|
| 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 |
0.581 |
|
| 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 |
0.457 |
|
| 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. DOI: 10.1021/Ja00270A005 |
0.491 |
|
| 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 |
0.459 |
|
| 1985 |
JORGENSEN WL, MADURA JD, SWENSON CJ. ChemInform Abstract: OPTIMIZED INTERMOLECULAR POTENTIAL FUNCTIONS FOR LIQUID HYDROCARBONS Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198508061 |
0.324 |
|
| 1984 |
Jorgensen WL, Madura JD, Swenson CJ. Optimized intermolecular potential functions for liquid hydrocarbons Journal of the American Chemical Society. 106: 6638-6646. DOI: 10.1021/Ja00334A030 |
0.469 |
|
| 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. DOI: 10.1063/1.445869 |
0.512 |
|
| 1983 |
Jorgensen WL, Madura JD. Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water Journal of the American Chemical Society. 105: 1407-1413. DOI: 10.1021/Ja00344A001 |
0.434 |
|
| 1983 |
Houk KN, Rondan NG, Brown FK, Jorgensen WL, Madura JD, Spellmeyer DC. Electronic origins and consequences of pyramidalization of asymmetric alkenes in ground and triplet excited states Journal of the American Chemical Society. 105: 5980-5988. DOI: 10.1002/Chin.198351060 |
0.386 |
|
| 1983 |
HOUK KN, RONDAN NG, BROWN FK, JORGENSEN WL, MADURA JD, SPELLMEYER DC. ChemInform Abstract: ELECTRONIC ORIGINS AND CONSEQUENCES OF PYRAMIDALIZATION OF ASYMMETRIC ALKENES IN GROUND AND TRIPLET EXCITED STATES Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198351060 |
0.303 |
|
| 1983 |
JORGENSEN WL, MADURA JD. ChemInform Abstract: QUANTUM AND STATISTICAL MECHANICAL STUDIES OF LIQUIDS. 25. SOLVATION AND CONFORMATION OF METHANOL IN WATER Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198338076 |
0.357 |
|
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