Publications of Mihaly Mezei

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(165) X.-Y. Meng, Y.XU, H.-X. Zhang, M. Mezei, M. Cui, Predicting Protein Interactions by Brownian Dynamics Simulations, Predicting Protein Interactions by Brownian Dynamics Simulations, accepted.     View Abstract
(164) M. D. Naidu, R. Agarwal, L. A. Pena, L. Cunha, M. Mezei, M. Shen, D. M. Wilson, III, Y. Liu, Z. Sanchez, P. Chaudhary, S. H. Wilson, M. J. Waring, Lucanthone and Its Derivative Hycanthone Inhibit Apurinic Endonuclease-1 (APE1) by Direct Protein Binding, PLoS ONE, 6, e23679 (2011).     View Abstract
(163) M. Mezei, Challenges in applying Monte Carlo sampling to biomolecular systems, in Innovations in Biomolecular Modeling, Royal Society of Chemistry, T. Schlick, ed., accepted.     View Abstract
(162) X.-Y. Meng, H.-X. Zhang, M. Mezei, M. Cui, Molecular Docking: A powerful approach for structure-based drug discovery, Current Computer-Aided Drug Design, accepted.     View Abstract
(161) M. Mezei, Discriminatory Power of Stoichiometry-Driven Protein Folding? J. Biomol. Struct. Dynam., 28, 625-626 (2011).    View Abstract Get Copy (Open access)
(160) M. Siatecka, K.E. Sahr, S.G. Andersen, M. Mezei, J.J. Bieker, and L.L. Peters, Sequence-selective disruption of EKLF zinc finger-DNA interactions: a unique mechanism of severe anemia in the Nan mutant mouse, Proc. Natl. Acad. Sci., 107, 15151-15156 (2010).    View Abstract Get Copy (Open access)
(159) M. Mezei, Simulaid: a simulation facilitator and analysis program, J. Comp. Chem., 31, 2658-2668 (2010).      View Abstract    Get Copy ($$$)
(158) M. Mezei and M.-M. Zhou, Dockres: a computer program that analyzes the output of virtual screening of small molecules, Source Code for Biology and Medicine, 5, 2 (2010).    View Abstract    Get Copy (Open access)
(157) D. Lupyan, M. Mezei, D.E. Logothetis, and R. Osman, A molecular dynamics investigation of lipid bilayer perturbation by PIP2., Biophys. J., 98, 240-247 (2010).    View Abstract
(156) K.D. Eichenbaum, Y. Rodriguez, M. Mezei, and R. Osman, The Energetics of the Acetylation Switch in p53-mediated Transcriptional Activation, Proteins,: Struct., Funct., and Bioinf., 78, 447-456 (2010).    View Abstract
(155) J.R. Banfelder, J.A. Speidel, and M. Mezei, Automatic determination of stepsize parameters in Monte Carlo simulations, tested on a bromodomain-binding octapeptide, Algorithms, 2, 215-226 (2009); doi:10.3390/a2010215.      View Abstract    Get Copy (Open access)

(154) P. Chaurasia, M. Mezei, M.-M. Zhou, and L. Ossowski, (2009) Computer aided identification of small molecules disrupting uPAR/a5B1 - integrin interaction; a new paradigm for metastasis prevention. PloS ONE,      View Abstract    Get Copy (Open access)
(153) Y. Rodriguez, M. Mezei, and R. Osman, Gla-domain binds to membrane through two dipalmitoylphosphatidylserines. A computational study. Biochemistry, 47, 3267 - 13278 (2008).    View Abstract
(152) M. Cui, M. Mezei, and R. Osman, Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field, Protein Eng. Des. Sel., 21, 729-735 (2008).    View Abstract
(151) A. Buku, I. Keselman, D. Lupyan, M. Mezei, J. Price, Effective Mast Cell Degranulating Peptide Inhibitors of the IgE/FceRI Receptor Interaction, Chem. Biol. & Drug Des, 72, 13-139 (2008).    View Abstract
(150) K. Gagnidze, Sachchidanand, R. Rozenfeld, M. Mezei, M.-M. Zhou, and L.A. Devi, Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2, J. Med. Chem., 51, 3378-3387 (2008).    View Abstract

(149) M. Cui, M. Mezei, and R. Osman, Modeling Dimerizations of Transmembrane Proteins using Brownian Dynamics Simulations, Journal of Computer-Aided Molecular Design, 22, 553-561 (2008).    View Abstract
(148) M. Mezei and M.-M. Zhou. Pspace: a program to plan the covering of a protein space. Source Code for Biology and Medicine, 2, 6 (2007). doi:10.1186/1751-0473-2-6    View Abstract    Get Copy (Open access)
(147) M. Mezei, Results from an Early Polarization Model Based on Maxwell's Invariant Multipole Form (invited contribution), J. Chem. Theory and Comp., 3, 2138-2145 (2007).    View Abstract
(146) L. Cunha, M. Kuti, D.F. Bishop, M. Mezei, L. Zeng, M.-M. Zhou, and R.J. Desnick, Human Uroporphyrinogen III Synthase: High Affinity Purification, NMR Resonance Assignments and Mapping of the Active Site NMR Studies Did Not Support a Heme Enzyme Complex. Proteins, 71, 855-873 (2007).    View Abstract
(145) A. Kentsis, T. Gindin, M. Mezei, R. Osman, (2007) Calculation of the Free Energy and Cooperativity of Protein Folding, PloS ONE, 2, e446. doi:10.1371/journal.pone.0000446      View Abstract    Get Copy (Open access)
(144) L.B. Partay, P. Jedlovszky, P.N.M. Hoang, S. Picaud and M. Mezei, Free Energy Profile of Small Solute Molecules at the Free Surfaces of Water and Ice, as Determined by Cavity Insertion Widom Calculations, J. Phys. Chem. C, 111, 9407-9416 (2007).      View Abstract
(143) C. Pan, M. Mezei, S. Mujtaba, M. Muller, L. Zeng, J. Li, Z. Wang, and M-M. Zhou, Structure-guided Optimization of Small Molecules Inhibiting Human Immunodeficiency Virus 1 Tat Association with the Human Coactivator p300/CREB Binding Protein-Associated Factor, J. Med. Chem., 50, 2285-2288 (2007).      View Abstract      
(142) K.D. Eichenbaum, M. Mezei, and J.W. Eichenbaum, Digital Contact Tonometry as an Aid in Contact Tonometry and Glaucoma Treatment, Annals of Ophthalmology, 39, 41-49 (2007).      View Abstract
(141) P. Jedlovszky, L. Partai, and M. Mezei, The Structure of the Zwitterionic Headgroups in a DMPC Bilayer as Seen from Monte Carlo Simulation: Comparison with ionic solutions. J. Molec. Liquids, 131-132, 225-234 (2007).      View Abstract
(140) Y. Rodriguez, M. Mezei, and R. Osman, Association free energy of dipalmitoylphosphatidylserines in a mixed dipalmitoylphosphatidylcholine membrane, Biophys. J., 92, 3071-3080 (2007).      View Abstract
(139) J A. Speidel, J.R. Banfelder, and M. Mezei, Automatic Control of Solvent Density in Grand Canonical Ensemble Monte Carlo Simulations, J. Chem. Theory and Comp., 2, 1429-1434 (2006). Journal site Abstract and Full text (with subscription or $$)      View Abstract
(138) M. Mezei, and P. Jedlovszky, Statistical Thermodynamics via Computer Simulation to Characterize Phospholipid Interactions in Membranes, in Membrane Lipid Protocols, A.M. Dopico, ed., Humana Press, Totowa, NJ, (2007) pp 127-144.      View Abstract       Preprint (PDF)
(137) M. Mezei and M. Filizola, TRAJELIX: A computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. J. Computer-Aided Molecular Design, 20, 97-107 (2006).      View Abstract
(136) M.G. Alinchenko, A.V. Anikeenko, V.P. Voloshin, N.N. Medvedev, M. Mezei, L. Pártay, and P. Jedlovszky, Effect of Cholesterol on the Properties of Phospholipid Membranes.4. Interatomic Voids. J. Phys. Chem. B, 109, 16490-16502 (2005).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(135) A. Kentsis, M. Mezei, and R. Osman, Origin of the Sequence Dependent Polyproline II Structure in Unfolded Peptides. Proteins, 61, 769-776 (2005).      View Abstract       Pub Med Abstract
(134) A. Buku, B.A. Condie, J.A. Price, and M. Mezei, [Ala12] MCD Peptide: a Lead Peptide to Inhibitors of IgE Binding to Mast Cell Receptors. Int. J. Pept. Res., 66, 132-137 (2005).       View Abstract       Pub Med Abstract
(133) M. Fuxreiter, M. Mezei, I. Simon, and R. Osman, Role of Interfacial Waters in Sequence Discrimination by BamHI, Biophys. J., 89, 903-911 (2005).      View Abstract       Pub Med Abstract
(132) P.J. Fleming, N.C. Fitzkee, M. Mezei, R. Srinivasan, and G.D. Rose, A Novel Method Reveals that Solvent Water Favors Polyproline II Over BETA-Strand Conformation in Peptides and Unfolded Proteins: Conditional Hydrophobic Accessible Surface Area (CHASA) Protein Science, 14, 111-118 (2005).      View Abstract       Pub Med Abstract
(131) M.G. Alinchenko, A.V. Anikeenko, N.N. Medvedev, V.P. Voloshin, M. Mezei, and P. Jedlovszky, Morophology of Voids in Molecular Systems. A Voronoi-Delaunay Analysis of a Simulated DMPC Membrane. J. Phys. Chem. B, 108, 19056-19067 (2004).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(130) A. Kentsis, M. Mezei, T. Gindin, and R. Osman, Unfolded State of Polyalanine is a Segmented Polyproline II Helix. Proteins, 55, 493-501 (2004).      View Abstract       Pub Med Abstract
(129) M. Mezei, P.J. Fleming, R. Srinivasan, and G.D. Rose, Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins, 55, 502-507 (2004).      View Abstract       Pub Med Abstract
(128) P. Jedlovszky, N.N. Medvedev, and M. Mezei, Effect of Cholesterol on the Properties of Phospholipid Membranes, 3. Local Lateral Structure. J. Phys. Chem. B, 108, 465-472 (2004).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(127) M. Mezei, A novel Fingerprint for the Characterization of Protein Folds, Prot. Engng., 16, 713-715 (2003).      View Abstract       Pub Med Abstract       Journal site Abstract and Full text (with subscription or $$)
(126) M. Mezei, An Other 'Clever' Idea Down the Drain ... #2. CCP5, Infoweb (http://www.ccp5.ac.uk/infoweb/infoweb_datemenu.shtml) (2003)      View Abstract       Full text
(125) P. Jedlovszky and M. Mezei, The Effect of Cholesterol on the Properties of Phospholipid Membranes. 2. Free Energy Profile of Small Molecules. J. Phys. Chem. B, 105, 5322-5332 (2003).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(124) P. Jedlovszky and M. Mezei, The effect of Cholesterol on the Properties of Phospholipid Membranes. 1. Structural Features. J. Phys. Chem. B, 105, 5311-5321 (2003).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(123) M. Mezei, Efficient Monte Carlo Sampling for Long Molecular Chains Using Local Moves, Tested on a Solvated Lipid Bilayer, J. Chem. Phys., 118, 3874-3879 (2003)      View Abstract       Journal site Abstract and Full text       Reprint (PDF)
(122) M. Mezei, A New Method for Mapping Macromolecular Topography, J. Mol. Graph. Model., 21, 463-472 (2003).      View Abstract       Pub Med Abstract      Preprint in PDF format
(121) A. Kentsis, M. Mezei, and R. Osman, MC-PHS: A Monte Carlo Implementation of the Primary Hydration Shell for Protein Folding and Design, Biophys. J., 84, 805-815 (2003).      View Abstract       Pub Med Abstract       Reprint in PDF format (posted with permission of the Biophysical Society)
(120) P. Jedlovszky, M. Mezei, and R. Vallauri, Comparison of Polarizable and Nonpolarizable Models of Hydrogen Fluoride in Liquid and Supercritical States. A Monte Carlo simulation study, J. Chem. Phys., 115, 9883-9894 (2001).      View Abstract       Journal site Abstract and Full text
(119) M. Mezei, On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies, in "Third International Workshop for Methods for Macromolecular Modeling Conference Proceedings", H.H. Gan and T. Schlick, eds., pp 177-198, Springer, New York (2002),      View Abstract      Manuscript TeX source       Preprint (PDF)
(118) M. Mezei, Free Energy Simulations Over Creation/Annihilation Paths for a Flexible Solute, Molecular Simulation, 28, 39-44 (2001).      View Abstract       Journal site Abstract and Full text       Preprint (PDF)
(117) P. Jedlovszky and M. Mezei, Orientational Order of the Water Molecules Across a Fully Hydrated DMPC Bilayer. A Monte Carlo Simulation Study, J. Phys. Chem. B, 105, 3614-3623 (2001).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(116) C.R. Watts, M. Mezei, R.F. Murphy, and S. Lovas, Conformational Space Comparison of GnRH and GnRH-III Using Molecular Dynamics and Cluster Analysis, J. Biomol. Struct. Dynam., 18, 733-748 (2001).      View Abstract       Pub Med Abstract
(115) H. Resat, and M. Mezei, Calculating the Local Solvent Chemical Potential in Crystal Hydrates, Phys. Rev. E, 62, 7031-7043 (2000).      View Abstract       Pub Med Abstract       Journal site Abstract       Full text (with subscription)      Reprint (PDF)
(114) P. Minary, P. Jedlovszky, M. Mezei, and L. Turi, A Comprehensive Liquid Simulation Study of Neat Formic Acid, J. Phys. Chem. B, 104, 8287-8294 (2000).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(113) M. Mezei, A Novel Approach to the Calculation of the Free Energy Due to Molecular Flexibility, J. Math. Chem., 27, 235-250 (2000).      View Abstract
(112) P. Jedlovszky and M. Mezei, Calculation of the Free Energy Profile of H2O,O2, CO, CO2, NO and CHCl3 in a Lipid Bilayer with a Cavity Insertion Variant of the Widom Method, J. Am. Chem. Soc., 122, 5125-5131 (2000).      View Abstract       Journal site Abstract and Full text (with subscription or $$)       Free access
(111) M. Mezei, Periodic Boundary Conditions: When is Eij ne Eji? Information Newsletter for Computer Simulation of Condensed Phases, CCP5, Daresbury Lab., No 47, (2000).      View Abstract       Full text
(110) M. Mezei, Finding of the Smallest Enclosing Cube to Improve Molecular Modeling, Information Newsletter for Computer Simulation of Condensed Phases, CCP5, Daresbury Lab., No 47, (2000).      View Abstract       Full text
(109) P. Jedlovszky, M. Mezei, and R. Vallauri, A Molecular Level Explanation of the Density Maximum of Liquid Water from Computer Simulations with a polarizable potential model, Chem. Phys. Letters, 318, 155-160 (2000).      View Abstract
(108) A.M. Sapse, M. Mezei, D.C. Jain, and C. Unson, Theoretical Studies of a Glucagon Fragment: Ser8-Asp9-Tyr10, Appendix in "Molecular orbital calculations for amino acids and peptides" by A.M. Sapse, Birkhäuser, Boston (2000).      View Abstract
(107) M. Mezei, Comment on "Molecular Dynamic Simulations in the Grand Canonical Ensemble: Formulation of a Bias Potential for umbrella sampling" Comparison of the Sampling Efficiency in the Grand Canonical Ensemble Using Molecular Dynamics and Cavity-Biased Monte Carlo, J. Chem. Phys., 112, 1059-1060 (2000).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(106) P. Jedlovszky and M. Mezei, Grand Canonical Ensemble Monte Carlo Simulation of a Lipid Bilayer Using Extension Biased Rotations, J. Chem. Phys., 111, 10770-10773 (1999).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(105) P. Jedlovszky and M. Mezei, Computer Simulation Study of Liquid CH2F2 with a New Effective Pair Potential Model. J. Chem. Phys., 110, 2991-3002 (1999).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(104) M. Mezei, and F. Guarnieri, Computer Simulation Studies of the Fully Solvated Wild-Type and Mutated GnRH in Extended and B-turn Conformations. J. Biomol. Struct. Dynam., 16, 723-732 (1998).      View Abstract       Pub Med Abstract       Journal site Abstract      Preprint in PDF format
(103) P. Jedlovszky and M. Mezei, The Anisotropic Virial-Biased Sampling for Monte Carlo Simulations in the Isobaric-Isothermal Ensemble. Mol. Phys., 96, 293-296 (1999).      View Abstract       Preprint (PDF)
(102) M. Mezei, Chameleon Sequences in the PDB, Prot. Engng., 11, 411-414 (1998).      View Abstract       Pub Med Abstract       Journal site Abstract        Reprint (PDF)
(101) A.M. Sapse, M. Mezei, I. Karakhanov and D.C. Jain, Solvent Effect on the Conformation of the Hoechst 33258 Agent. J. Molecular Struct. (Theochem), 393, 25-30 (1997).      View Abstract       Preprint (PDF)
(100) M. Mezei, Optimal Position of the Solute for Simulations. J. Comp. Chem., 18, 812-815 (1997).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(99) H. Resat, P.V. Maye, and M. Mezei, The Sensitivity of Conformational Free Energies of Alanine Dipeptide to Atomic Site Charges. Biopolymers, 41, 73-81 (1997).      View Abstract       Pub Med Abstract
(98) F. Guarnieri, and M. Mezei, Simulated Annealing of the Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Groove of DNA. J. Am. Chem. Soc., 118, 8493-8494 (1996).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(97) H. Resat, and M. Mezei, Grand Canonical Ensemble Monte Carlo Simulation of the dCpG/Proflavine Crystal Hydrate. Biophys. J., 71, 1179-1190 (1996).      View Abstract       Pub Med Abstract       Journal site Abstract
(96) H. Resat, M. Mezei, and J.A. McCammon, Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations. J. Phys. Chem., 100, 1426-1432 (1996).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(95) P.V. Maye, and M. Mezei, Calculation of the Free Energy of Solvation of the Li+ and Na+ Ions in Water and Chloroform. J. Molecular Struct. (Theochem), 362, 317-324 (1996).      View Abstract      Preprint (PDF)
(94) H. Sun, M. Mezei, R. Fye, and C.J. Benham, Monte Carlo Analysis of Conformational Transitions in Superhelical DNA. J. Chem. Phys., 103, 8653-8665 (1995).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(93) M. Mezei, and G. Jancsó, Free-Energy Simulation Studies on the Hydration of Tetramethylurea and Tetramethylthiourea. Chem. Phys. Letters, 239, 237-240 (1995).      View Abstract
(92) R. Friedman and M. Mezei, The Sensitivities of Interionic Potential of Mean Forces Studied by Adaptive Umbrella Sampling. J. Chem. Phys., 102, 419-426 (1995).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(91) H. Resat, and M. Mezei, Grand Canonical Monte Carlo Simulation of Water Positions in Crystal Hydrates. J. Am. Chem. Soc., 116, 7451-7452 (1994).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(90) H. Resat, and M. Mezei, Studies on the Free Energy Calculations. II. Theoretical Approaches to Molecular Solvation. J. Chem. Phys., 101, 6126-6140 (1994).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(89) M. Mezei, and K. Bencsáth, Long-Range Contribution to Inverse-Distance and Morse Energy and Pressure Terms of a Molecular Liquid, Tested on Benzene. J. Math. Chem., 16, 61-71 (1994).      View Abstract
(88) A.M. Sapse, M. Mezei, D.C. Jain, and C. Unson, An Ab Initio Study of Aspartic Acid and Glutamic Acid: Supplementary Evidence of Structural Requirements at Position 9 for Glucagon Activity. J. Molecular Struct. (Theochem), 306, 225-233 (1994).      View Abstract
(87) M. Mezei, A Heuristic Procedure for the Detection of Locally Similar Substructures of Two Equivalent Structures. Prot. Engng., 7, 331-333 (1994).      View Abstract       Pub Med Abstract       Journal site Abstract
(86) M. Mezei, Iso-Energy Cutoff for the Calculation of Interionic Potential of Mean Force in Water. Int. J. Quant. Chem., 52, 147-152 (1994).      View Abstract       Preprint (PDF)
(85) H. Resat, and M. Mezei, Studies in the Free Energy Calculations. I. Thermodynamic Integration Using a Polynomial Path. J. Chem. Phys., 99, 6052-6061 (1993).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(84) M. Mezei, The Case for Keeping Simulated Clusters Spherical. Information Quarterly, CCP5, Daresbury Lab., No 37, 38-40 (1993).      View Abstract       Full text
(83) M. Mezei, The Effect of the Combined Volume on the Efficiency of Gibbs ensemble Simulations, Molecular Simulation, 11, 395-397 (1994).      View Abstract       Preprint (PDF)
(82) M. Mezei, An Other 'Clever' Idea Down the Drain ... Information Quarterly, CCP5, Daresbury Lab., No 36, 24 (1993).      View Abstract       Full text
(81) M. Mezei, Calculation of Solvation Free Energy Differences for Large Solute Change from Computer Simulations with Quadrature-Based Nearly Linear Thermodynamic Integration. Molecular Simulation, Special issue, invited contribution 10, 225-240 (1993).      View Abstract
(80) M. Mezei, Theoretical Calculation of the Liquid-Vapor Coexistence Curve of Water, Chloroform and Methanol with the Cavity-Biased Monte Carlo Method in the Gibbs Ensemble, Molecular Simulation, 9, 257-267 (1992).      View Abstract       Preprint (PDF)
(79) M. Mezei, Efficient Calculation of the Pressure in the Canonical Ensemble for Inverse Power Central Forces, Information Quarterly, CCP5, Daresbury Lab., No 34, 46-47 (1992).      View Abstract       Full text
(78) M. Mezei, Determining Nearest Image in non-Orthogonal Periodic Systems, Information Quarterly, CCP5, Daresbury Lab., No 34, 48-51 (1992).      View Abstract       Full text
(77) M. Mezei, Polynomial Path for the Calculation of Liquid State Free Energies from Computer Simulations Tested on Liquid Water, J. Comp. Chem., 13, 651-656 (1992).      View Abstract       Preprint (PDF)
(76) M. Mezei, Free-Energy Simulations for the Study of Proton Transfer in Solutions, Proton Transfer in Hydrogen-Bonded Systems, 273-280, T. Bountis, ed., Plenum, New York (1992).      View Abstract       Preprint (PDF)
(75) M. Mezei, On the Possibility of Obtaining an Effective Pairwise Additive Intermolecular Pontential via an Ab-initio Route by Fitting to a Cooperative Model of Condensed Phase Configurations, J. Phys. Chem., 95, 7043-7049 (1991).      View Abstract
(74) J.J. Dannenberg, and M. Mezei, Reply to the Comment on the Application of Basis Set Superposition Error to ab Initio Calculation of Water Dimer, J. Phys. Chem., 95, 6396-6398 (1991).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(73) T. Schlik, S. Figueroa, and M. Mezei, A Molecular Dynamics Simulation of a Water Droplet by the Implicit-Euler/Langevin Scheme, J. Chem. Phys., 94, 2118-2130 (1991).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(72) M. Mezei, Distance-Scaled Force Biased Monte Carlo Simulation for Solutions Containing a Strongly Interacting Solute, Molecular Simulation, 5, 405-408 (1991).      View Abstract       Preprint (PDF)
(71) M. Mezei, The Theory of Hydrogen Bonding in Water, Physics of Many-Particle Systems, Vol. 19, 37-50, E.S. Kryachko, ed., Naukova Dumka, Kiev (1991).      View Abstract       Preprint (PDF)
(70) M. Mezei, and A. Ben-Naim, Calculation of the Solvent Contribution to the Potential of Mean Force Between Water Molecules in Fixed Relative Orientation in Liquid Water, J. Chem. Phys., 92, 1359-1361 (1990).      View Abstract       Journal site Abstract and Full text      Reprint (PDF)
(69) M.S. Broido, and M. Mezei, Computational analysis of the Effects of Site-Specific Phosphate Alkylation in the DNA Oligomer, {d-[GGAATTCC]}2 Biopolymers, 29, 597-607 (1990).      View Abstract       Pub Med Abstract       Preprint (PDF)
(68) M. Mezei, Evaluation of the Adaptive Umbrella Sampling Method, Molecular Simulation, 3, 301-313 (1989).      View Abstract       Preprint (PDF)
(67) M. Mezei, and J.J. Dannenberg, An Evaluation of Water-Water Analytical Potentials in the Region of Low Energy Trifurcated Structures, J. Phys. Chem., 92, 5860-5861 (1988).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(66) M. Mezei, Direct Calculation of the Excess Free Energy of the Dense Lennard-Jones Fluid with Nonlinear Thermodynamic Integration, Molecular Simulation, 2, 201-207 (1989).      View Abstract       Preprint (PDF)
(65) M. Mezei, Test of the Overlap Ratio Method on the Calculation of the Aqueous Hydration Free Energy Difference Between Acetone and Dimethyl Amine, Mol. Phys., 65, 219-223 (1988).      View Abstract       Preprint (PDF)
(64) M. Mezei, Modified Proximity Criterion for the Analysis of the Solvation Environment of a Polyfunctional Solute, Molecular Simulation, 1, 327-332 (1988).      View Abstract       Preprint (PDF)
(63) M. Mezei, Near-Neighbour Algorithm in Metropolis Monte Carlo Simulations, Molecular Simulation, 1, 169-171 (1988).      View Abstract       Preprint (PDF)
(62) B. Jayaram, M. Mezei, and D.L. Beveridge, Conformational Stability of the Dimethylphosphate Anion in Water: Liquid State Free Energy Simulations, J. Am. Chem. Soc., 110, 1691-1694 (1988).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(61) M. Mezei, K. Bencsáth, Long-Range Contribution to Inverse-Distance and Morse Energy S. Goldman, and S. Singh, The Detailed Balance Energy-Scaled Displacement Monte Carlo Algorithm, Molecular Simulation, 1, 87-93 (1987).      View Abstract       Preprint (PDF)
(60) M. Mezei, The Finite Difference Thermodynamic Integration, Tested on Calculating the Hydration Free Energy Difference Between Acetone and Dimethylamine in Water, J. Chem. Phys., 86, 7084-7088 (1987).      View Abstract       Journal site Abstract     Reprint (PDF)
(59) B. Jayaram, M. Mezei, and D.L. Beveridge, Monte Carlo Study of the Aqueous Hydration of Dimethyl Phosphate in the gg, gt and tt Conformations, J. Comp. Chem., 8, 917-942 (1987).      View Abstract
(58) M. Mezei, Grand-Canonical Ensemble Monte Carlo Simulation of Dense Fluids: Lennard-Jones, Soft Spheres and Water, Mol. Phys., 61, 565-582 (1987); Erratum, 67, 1207-1208 (1989).      View Abstract       Preprint (PDF)
(57) M. Mezei, A Comment on Debugging Monte Carlo Programs, Information Quarterly, CCP5, Daresbury Lab., No 23, 33-37 (1986).      View Abstract       Full text
(56) Reprint with permission of (48), Int. J. Quant. Chem., XXIX, 1513-1523 (1986).      View Abstract
(55) M. Mezei, S.W. Harrison, G. Ravishanker, and D.L. Beveridge, Monte Carlo Studies of the Aqueous Hydration of Cis and Trans N-Methyl-Acetamide: Sensitivity of Results to Convergence and to Choice of Intermolecular Potential Functions, Israel J. of Chem., 27, 163-172 (1986).      View Abstract
(54) M. Mezei, and D.L. Beveridge, Free Energy Simulations, Ann. Acad. Sci N.Y., 482, 1-23 (1986).      View Abstract       Preprint (PDF)
(53) M. Mezei, Adaptive Umbrella Sampling: Self-Consistent Determination of the Non-Boltzmann Bias, J. Comp. Phys. 68, 237-248 (1987).      View Abstract       Preprint (PDF)
(52) E.S. Campbell, and M. Mezei, An Algorithm for the Calculation of the Net Induction Energy and Induced Multipole Tensors in a Set of Charge Distributions with Non-Linear Contributions of All Potentials of External Fields and Both Permanent and Induced Multipoles, Mol. Phys., 57, 1201-1218 (1986).      View Abstract
(51) G. Ravishanker, M. Mezei, and D.L. Beveridge, Conformational Stability and Flexiblity of the Ala Dipeptide in Free Space and Water: Monte Carlo Computer Simulation Studies, J. Comp. Chem., 7, 345-348 (1986).      View Abstract
(50) D.L. Beveridge, G. Ravishanker, M. Mezei, and B. Gedulin, Solvent Effect on Conformational Stability in the Ala Dipeptide: Full Free Energy Simulations, J. Biomol. Struct. Dynam., III, 237-252 (1986).      View Abstract
(49) M. Mezei, and D.L. Beveridge, Structural Chemistry of Biomolecular Hydration via Computer Simulation: The Proximity Criterion, Methods in Enzymology, 127, L. Packer, ed., 22-47 (1985).      View Abstract
(48) D.L. Beveridge, M. Mezei, G. Ravishanker, and B. Jayaram, Free Energy Simulations: Applications to the Study of Liquid Water, Hydrophobic Interactions and Solvent Effects on Conformational Stability,      View Abstract J. of Biosciences, 8, 167-178 (1985).
(47) D.L. Beveridge, and M. Mezei, Free Energy Simulations: The Coupling Parameter Approach and Topographical Transition Coordinates, in the Proceedings of a Workshop on Molecular Dynamics and Protein Structure, J. Hermans and W. van Gunsteren, eds., Polycrystal Book Services, Crystal Springs, Ill. (1985).      View Abstract
(46) M. Mezei and R.J. Speedy, Pentagon-Pentagon Correlations in Water, J. Phys. Chem., 89, 171-175 (1985).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(45) M. Mezei, P.K. Mehrotra, and D.L. Beveridge, Monte Carlo Determination of the Free Energy and Internal Energy of Hydration for the Ala Dipeptide at 25oC, J. Am. Chem. Soc., 107, 2239-2245 (1985).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(44) M. Mezei and R.J. Speedy, Simulation Studies of the Dihedral Angle in Water, J. Phys. Chem., 88, 3180-3182 (1984).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(43) M. Mezei, and D.L. Beveridge, Generic Solvation Sites in a Crystal, J. Comp. Chem., 6, 523-527 (1984).      View Abstract       Preprint (PDF)
(42) P.K. Mehrotra, M. Mezei, and D.L. Beveridge, Monte Carlo Determination of the Internal Energies of Hydration for the Ala Dipeptide in the C7, C5, aR and PII Conformations, Int. J. Quant. Chem., 11, 301-308 (1984).      View Abstract
(41) D.L. Beveridge, P.V. Maye, B. Jayaram, G. Ravishanker, and M. Mezei, Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation Studies, J. Biomol. Struct. Dynam., 2, 261-270 (1984).      View Abstract       Pub Med Abstract
(40) G. Ravishanker, P.K. Mehrotra, M. Mezei, and D.L. Beveridge, Aqueous Hydration of Benzene, J. Am. Chem. Soc., 106, 4102-4108 (1984).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(39) M. Mezei, P.K. Mehrotra, and D.L. Beveridge, Aqueous Hydration of the Glycine Zwitterion, J. Biomol. Struct. Dynam., 2, 1-27 (1984).      View Abstract       Pub Med Abstract
(38) M. Mezei, D.L. Beveridge, H.M. Berman, J.M. Goodfellow, J.L. Finney, and S. Neidle, Monte Carlo Studies on Water in the dCpG/Proflavin Crystal Hydrate, J. Biomol. Struct. Dynam., 1, 287-297 (1983).      View Abstract      Full text       Pub Med Abstract
(37) M. Mezei, Comparison of the Percolation Model with the Computer Simulation Results on Different Water Models, Mol. Phys., 52, 1003-1010 (1984).      View Abstract
(36) D.L. Beveridge, G. Ravishanker, and M. Mezei, Solvent Separated Hydropobic Interactions, in "Structure and Dynamics of Proteins and Nucleic Acids", E. Clementi, ed., Adenine Press, New York, 477-483 (1983).      View Abstract
(35) D.L. Beveridge, M. Mezei, P.K. Mehrotra, F.T. Marchese, G. Ravishanker, T. Vasu, and S. Swaminathan, Monte Carlo Computer Simulation Studies of the Equilibrium Properties and Structure of Liquid Water, in "Molecular-Based Study and Prediction of Fluid Properties", J.M. Haile, and G.A. Mansoori, eds., (American Chemical Society) Vol. 204, 297-351 (1983).      View Abstract
(34) M. Mezei, Virial-Bias Monte Carlo Methods: Efficient Sampling in the (T,P,N) Ensemble, Mol. Phys., 48, 1075-1082 (1983).      View Abstract
(33) D.L. Beveridge, G. Ravishanker, and M. Mezei, Monte Carlo Computer Simulation Study of the Hydrophobic effect: Potential of Mean Force for [(CH4)2]aq at 25oC and 50oC, J. Chem. Soc. Faraday Trans., 17, 79-91 (1982).      View Abstract
(32) M. Mezei, Excess Free Energy of Different Water Models Computed by Monte Carlo Methods, Mol. Phys., 47, 1307-1315 (1982); Erratum, 67, 1205-1206 (1989).      View Abstract
(31) P.K. Mehrotra, M. Mezei, and D.L. Beveridge, Convergence Acceleration in Monte Carlo Computer Simulation on Water and Aqueous Solutions, J. Chem. Phys., 78, 3156-3166 (1983).      View Abstract       Journal site Abstract and Full text       Reprint (PDF)
(30) E.S. Campbell, and M. Mezei, Torque Algorithms: The Permanent Multipole and Induced Dipole Vector Contributions in a Set of Charge Distributions, J. Comp. Phys. 47, 245-257 (1982).      View Abstract
(29) P.K. Mehrotra, M. Mezei, and D.L. Beveridge, Preliminary Results on Convergence Acceleration in Monte Carlo Computer Simulation on Water and Aqueous Solutions, Proceedings of a Conference on Organic and Biological Molecules, NRCC, University of California, Berkeley, 63-73 (1981).      View Abstract
(28) M. Mezei, and D.L. Beveridge, Further Quasicomponent Distribution Function Analysis of Liquid Water. Temperature Dependence of the Results, J. Chem. Phys., 76, 593-600 (1982).      View Abstract       Journal site Abstract       Reprint (PDF)
(27) M. Mezei, and D.L. Beveridge, Monte Carlo Studies of the Structure of Dilute Aqueous Solution of Li+, Na+, K+, F-, Cl- Ions, J. Chem. Phys., 74, 6902-6910 (1981).      View Abstract       Journal site Abstract       Reprint (PDF)
(26) D.L. Beveridge, M. Mezei, P.K. Mehrotra, F.T. Marchese, T.R. Vasu, and G. Ravishanker, Liquid State Computer Simulation Studies of Biomolecular Solvation Problems, Ann. N.Y. Acad. Sci., 367, 108-131 (1981).      View Abstract
(25) M. Mezei, and D.L. Beveridge, Theoretical Studies of Hydrogen Bonding in Liquid Water and Dilute Aqueous Solutions. J. Chem. Phys., 74, 622-632 (1981).      View Abstract       Journal site Abstract and Full text       Reprint (PDF)
(24) E.S. Campbell and M. Mezei, A cooperative calculation and analysis of electric fields, induced dipole vectors and lattice energies for rotationally ordered ices IX, II and disordered Ih, Mol. Phys., 41, 883-905 (1980).      View Abstract
(23) M. Mezei, On the Selection of the Particle to be Perturbed in the Monte Carlo Method, J. Comp. Phys. 39, 128-136 (1981).      View Abstract       Preprint (PDF)
(22) M. Mezei, Estimation of the Difference Between Molecular Dynamics and Monte Carlo Averages Due to the Truncation of the Potential, Chem. Phys. Letters, 74, 105-107 (1980).      View Abstract
(21) M. Mezei, A Cavity-Biased (T,V,m) Monte Carlo Method for the Computer Simulation of Fluids, Mol. Phys., 40, 901-906 (1980).      View Abstract
(20) M. Mezei, S. Swaminathan, D.L. Beveridge, Convergence Characteristics of the Conventional Metropolis Monte Carlo Method on Liquid Water, J. Chem. Phys., 71, 3366-3373 (1979).      View Abstract       Journal site Abstract and Full text       Reprint (PDF)
(19) D.L. Beveridge, M. Mezei, S. Swaminathan, and S.W. Harrison, Monte Carlo Studies of the Structure of Liquid Water and Dilute Aqueous Solutions. "Computer Modeling of Matter", P.G. Lykos, ed.; ACS Symposium Series, 86, 191-218 American Chemical Society, Washington D.C. (1978).      View Abstract
(18) E.S. Campbell, and M. Mezei, Computer Algorithms and Programs for Permanent Multipole and Induced Dipole Vectors in Crystals, J. Comp. Phys. 29, 297-301 (1978).      View Abstract
(17) M. Mezei, S. Swaminathan, and D.L. Beveridge, Ab Initio Calculation of the Free Energy of Water, J. Am. Chem. Soc., 100, 3255-3256 (1978).      View Abstract       Journal site Abstract and Full text (with subscription or $$)
(16) E.S. Campbell, and M. Mezei, Use of a non Pair-Additive Intermolecular Potential Function to Fit Quantum-Mechanical Data on Water Molecule Interactions, J. Chem. Phys., 67, 2338-2344 (1977).      View Abstract       Journal site Abstract and Full text       Preprint (PDF)
(15) M. Mezei, and E.S. Campbell, Efficient Multipole Expansion: Choice of Order and Density Partitioning Techniques, Theoret. Chim. Acta (Berl.), 43, 227-237 (1977).      View Abstract       Preprint (PDF)
(14) E.S. Campbell, and M. Mezei, Efficient Construction of Directional Derivatives of a Function of a Vector Magnitude and Maxwell's Invariant Multipole Form, J. Comp. Phys. 21, 114-122 (1976).      View Abstract       Preprint (PDF)
(13) M. Mezei, and E.S. Campbell, A Computational Procedure for Obtaining the Poles of a Spherical Harmonics of Order N; Application to the Multipole Expansion of Electrostatic Interaction, J. Comp. Phys. 20, 110-116 (1976).      View Abstract       Preprint (PDF)
(12) M. Mezei, New Approximate Solution of the Spin-Free Schrodinger Equation, Advantageous on a not One-Particle Basis Set, Phys. Rev. A, 13, 23-26 (1976).
(11) Zs. Esztergár, and M. Mezei, A számitástechnika kémiai alkalmazása, (Computers in Chemistry), III, Az Algol programozási nyelv (The Algol programming language) Magyar Kémikusok Lapja (Journal of the Hungarian Chemists'), 28, 142-151 (1973).    View Abstract
(10) P. Benedek, and M. Mezei, A számitástechnika kémiai alkalmazása, (Computers in Chemistry), II, Számitási algoritmus,számitási folyamatábra (Computational algorithm, computational flow chart), Magyar Kémikusok Lapja (Journal of the Hungarian Chemists'), 28, 99-103 (1973);    View Abstract
(9) P. Benedek, and M. Mezei, A számitástechnika kémiai alkalmazása, (Computers in Chemistry), I, Az elektronikus számitógépekröl (On the electronic computers), Magyar Kémikusok Lapja (Journal of the Hungarian Chemists'), 28, 29-35 (1973)    View Abstract
(8) M. Mezei, The Error of a Function Approximation Based on Random Selected Points, J. Inst. Maths. Applics., 12, 97-102 (1973).    View Abstract    Full text
(7) M. Mezei, and T. Szondy, On the Possibility of Replacing the Backward Transformation of the Modified Simplex Method by a Forward Transformation, J. Inst. Maths. Applics., 11, 339-342 (1973).    View Abstract    Full text
(6) T. Szondy, M. Hegyi, V. Lengyel, M. Mezei, and E. Kapuy, Determination of Many-Particle Integrals by the Method of Distance Functions, Theoret. Chim. Acta (Berl.), 33, 249-261 (1974).    View Abstract
(5) M.G. Hegyi, M. Mezei, and T. Szondy, Determination of Molecular Properties by the Method of Moments, III, Theoret. Chim. Acta (Berl.), 21, 168-175 (1971).    View Abstract
(4) M.G. Hegyi, M. Mezei, and T. Szondy, Determination of Molecular Properties by the Method of Moments, II, Theoret. Chim. Acta (Berl.), 15, 283-292 (1969).    View Abstract
(3) M.G. Hegyi, M. Mezei, and T. Szondy, Determination of Molecular Properties by the Method of Moments, I, Theoret. Chim. Acta (Berl.), 15, 273-282 (1969).    View Abstract
(2) M. Mezei, and P. Pulay, Calculation of Force Constants with the Maximum Overlap Method, Acta Chimica Acad. Sci. Hungaricae,. 57, 331-335 (1968).    View Abstract    Full text
(1) M. Mezei, and P. Pulay, Calculation of Force Constants with the Maximum Overlap Method, Acta Chimica Acad. Sci. Hungaricae, 56, 167-173 (1968)    View Abstract    Full text
(0) M. Mezei, Studies With the Local Energy Method (Ph.D. Thesis)      View Abstract       Preprint (PDF)
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Last modified: 19/18/2011 (MM)