101. Dutta A., Lazaridis T. “Classical Models of Hydroxide for Proton Hopping Simulations”, J. Phys. Chem. B, 128, 12161-12170 (2024) (link)
100. Hwang W. et al. “CHARMM at 45: Enhancements in accessibility, functionality, and speed”, J. Phys. Chem. B, 128, 9976-10042 (2024) (link)
99. Maurer M., Lazaridis T. “Transmembrane β‑Barrel Models of α‑Synuclein Oligomers”, J. Chem. Inf. Model., 63, 7171-7179 (2023) (link)
98. Rodriguez S.Y.V, Lazaridis T. “Simulations suggest a scaffolding mechanism of membrane deformation by the caveolin 8S complex”, Biophys. J..,122, 4082-90 (2023) (link)
97. Maurer M., Lazaridis T. “Comparison of classical and ab initio simulations of hydronium and aqueous proton transfer”, J. Chem. Phys.,127, 134506 (2023) (link)
96. Lazaridis T. “Proton Paths in Models of the Hv1 Proton Channel”, J. Phys. Chem. B,127, 7937−7945 (2023) (link)
95. Dutta A., Sepehri A., Lazaridis T. “Putative Pore Structures of Amyloid β 25−35 in Lipid Bilayers”, Biochemistry, 62, 2549−2558 (2023) (link)
94. Sepehri A., Lazaridis T. “Putative Structures of Membrane-Embedded Amyloid β Oligomers”, ACS Chemical Neuroscience, 14:99-110 (2023) (link)
93. Lazaridis T. “Molecular origins of asymmetric proton conduction in the influenza M2 channel”, Biophysical Journal, 122: 90-98 (2023) (link)
92. Lazaridis T., Sepehri A. “Amino acid deprotonation rates from classical force fields”, J Chem Phys, 157: 085101 (2022) (link)
91. Sepehri A., Nepal B., Lazaridis T. “Distinct Modes of Action of IAPP Oligomers on Membranes”, J Chem Inf Model, 61:4645-4655 (2021) (link)
90. Nepal B., Sepehri A., Lazaridis T. “Mechanism of negative membrane curvature generation by I-BAR domains”, Structure, 29:1440-1452 (2021) (link)
89. Sepehri A., Nepal B., Lazaridis T. “Lipid interactions of an actinoporin pore-forming oligomer”, Biophys. J. 120:1357-1366 (2021) (link)
88. Dixit M., Lazaridis T. “Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint”, J. Chem. Phys. 153: 054101 (2020) (link)
87. Magana M., Pushpanathan M., Santos A.L., Leanse L., Fernandez M., Ioannidis A., Giulianotti M.A., Apidianakis Y., Bradfute S., Ferguson A.L., Cherkasov A., Seleem M.N., Pinilla C., de la Fuente-Nunez C., Lazaridis T., Dai T., Houghten R.A., Hancock R.E.W., Tegos G.P., “The value of antimicrobial peptides “, The Lancet Inf. Dis. 20:E216-R230 (2020) (link)
86. Rodnin M.V., Vasquez-Montes V., Nepal B., Ladokhin A.S., Lazaridis T., “Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers”, J. Mem. Biol. 253:287-98 (2020) (link)
85. Zhang Y., Haider K., Kaur D., Ngo V.A., Cai X., Mao J., Khaniya U., Zhu X., Noskov S., Lazaridis T., Gunner M.R. ” Characterizing the water wire in the gramicidin channel found by Monte Carlo sampling using continuum electrostatics and in Molecular Dynamics trajectories with conventional or polarizable force fields”, J. Comp. Bioph. Chem. 20:111-130 (2021) (link)
84. Nepal B., Sepehri A., Lazaridis T. “Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7”, Pro. Sci., 29:1473-85 (2020) (link)
83. Sepehri A., PeBenito L, Pino-Angeles A., Lazaridis T. “What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives”, Biophys. J., 118:1901-13 (2020) (link)
82. Pino-Angeles A., Lazaridis T. “Effects of peptide charge, orientation, and concentration on melittin transmembrane pores”, Biophysical J, 114:2865 (2018) (link)
81. Nepal B., Leveritt J. III, Lazaridis T. “Membrane curvature sensing by amphipathic helices: Insights from implicit membrane modeling”, Biophysical J, 114:2128 (2018) (link)
80. Lazaridis T., Hummer G. “Classical Molecular Dynamics with Mobile Protons”, J. Chem. Inf. Mod, 57:2833-45 (2017) (link)
79. Lipkin R., Pino-Angeles A., Lazaridis T. “Transmembrane Pore Structures of beta-Hairpin Antimicrobial Peptides by All-Atom Simulations”, J. Phys. Chem. B, 121:9126-40 (2017) (link)
78. Lipkin R., Lazaridis T. “Computational studies of peptide-induced membrane pore formation”, Phil. Trans. R. Soc. B, 372:20160219 (2017) (link)
77. Lipkin R., Lazaridis T. “Computational prediction of the optimal oligomeric state for membrane-inserted b-barrels of protegrin-1 and related mutants”, J Pep Sci, 23:334-45 (2017) (link)
76. Pino-Angeles A.,Leveritt J.M. III, Lazaridis T. “Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family”, PLOS Comp. Biol. 12:e1004570 (2016) (link)
75. Versace R., Lazaridis T. “Modeling Protein-Micelle Systems in Implicit Water”, J. Phys. Chem. B, 119:8037-47 (2015) (link)
74. Leveritt J.M. III, Pino-Angeles A., Lazaridis T. “The Structure of a Melittin-Stabilized Pore”, Biophys J, 108:2424-6 (2015) (link)
73. Lipkin R.B., Lazaridis T. “Implicit Membrane Investigation of the Stability of Antimicrobial Peptide beta-barrels and arcs”, J Mem Biol, 248:469-86 (2015) (link)
72. Brice A., Lazaridis T. “Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR”, J. Phys. Chem. B, 118:4461-70 (2014) (link)
71. Lazaridis T., Versace R. “The treatment of solvent in multiscale biophysical modeling”, Isr. J. Chem., 54:1074-83 (2014) (link)
70. Lazaridis T., Leveritt JM, PeBenito L. “Implicit membrane treatment of buried charged groups. Application to peptide translocation across lipid bilayers”, BBA Biomembranes, 1838:2149-59 (2014) (link)
69. Prieto L., He Y., Lazaridis T. “Protein arcs may form stable pores in membranes”, Biophys J, 106:154-161 (2014) (link)
68. Rahaman A., Lazaridis, T. “A thermodynamic approach to alamethicin pore formation”, BBA Biomembranes 1838:98 (2014) (link) Erratum: link
67. He Y., Lazaridis, T. “Activity Determinants of Helical Antimicrobial Peptides: A Large-scale Computational Study”, PLOS One, 8(6): e66440 (2013) (link)
66. He Y., Prieto L., Lazaridis, T. “Modeling Peptide Binding To Anionic Membrane Pores”, J Comp Chem, 34:1463-75 (2013) (link)
65. Lazaridis, T., He Y., Prieto L. “Membrane interactions and pore formation by the antimicrobial peptide protegrin”, Biophysical J, 104:633-42 (2013) (link)
64. Zhan H., Lazaridis, T. “Inclusion of Lateral Pressure/Curvature Stress Effects in Implicit Membrane Models”, Biophysical J, 104:643-54 (2013) (link)
63. Yuzlenko O., Lazaridis, T. “Membrane protein native state discrimination by implicit membrane models”, J Comp Chem, 34:731-8 (2013) (link)
62. Lazaridis, T. “The hydrophobic effect”, in Encyclopedia of Life Sciences, Wiley, (2013) (link)
61. Mihajlovic, M., Lazaridis, T. “Charge Distribution and Imperfect Amphipathicity Affect Pore Formation by Antimicrobial Peptides”, BBA-Biomembranes , 1818:1274-83 (2012) (link)
60. Lazaridis, T. “Ligand and Receptor Conformational Energies, in Protein-ligand interactions (Gohlke, H., Ed.), Wiley (2012)
59. Li, Z., Lazaridis, T. “Computing the thermodynamic contributions of interfacial water”, Methods in Molecular Biology, 819:393-404 (2012) (link)
58. Zhan H., Lazaridis, T. “Influence of the membrane dipole potential on peptide binding to lipid bilayers”, Biophys Chem, 161:1-7 (2012) (link)
57. Yuzlenko O., Lazaridis, T. “Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface”, J Phys Chem B, 115:13674-84 (2011) (link)
56. Madeo J., Mihajlovic M., Lazaridis T., Gunner M.R. “Slow Dissociation of a Charged Ligand: Analysis of the Primary Quinone QA Site of Photosynthetic Bacterial Reaction Centers”, J Am Chem Soc, 133:17375-85 (2011) (link)
55. Ramos J., Lazaridis, T. “Computational analysis of residue contributions to coiled-coil topology”, Protein Science, 20:1845-55 (2011) (link)
54. Prieto L., Lazaridis, T. “Computational studies of colicin insertion into membranes: The closed state”, Proteins, 79:126-141 (2011) (link)
53. Mihajlovic, M., Lazaridis, T. “Antimicrobial Peptides in Toroidal and Cylindrical Pores”, BBA-Biomembranes , 1798:1485-1493 (2010) (link)
52. Mihajlovic, M., Lazaridis, T. “Antimicrobial peptides bind more strongly to membrane pores”, BBA-Biomembranes , 1798:1494-1502 (2010) (link)
51. Brooks, BR. et al. “CHARMM: The Biomolecular Simulation Program”, J. Comp. Chem. , 30: 1545-1614 (2009)
50. Zhang, JM., Lazaridis, T. “Transmembrane Helix Association Affinity Can Be Modulated by Flanking and Noninterfacial Residues”, Biophys. J. , 96:4418-27 (2009)
49. Hajjar, E., Mihajlovic, M., Witko-Sarsat, V., Lazaridis, T., Reuter, N. “Computational prediction of the binding site of proteinase 3 to the plasma membrane”, Proteins , 71:1655-69 (2008)
48. Mihajlovic, M., Lazaridis, T. “Membrane-bound structure and energetics of alpha-synuclein”, Proteins , 70:761-78 (2008)
47. Mihajlovic, M., Lazaridis, T. “Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane”, Prot. Sci. , 16:2042-55 (2007)
46. Li, Z., Lazaridis, T. “Water at biomolecular binding interfaces”, Phys. Chem. Chem. Phys. , 9:573-81 (2007)
45. Sammalkorpi, M., Lazaridis, T. “Modeling a spin labeled fusion peptide in a membrane: Implications for the interpretation of EPR experiments”, Biophys. J. , 92:10-22 (2007)
44. Sammalkorpi, M., Lazaridis, T. “Configuration of influenza hemagglutinin fusion peptide monomers and oligomers in membranes”, BBA Biomembranes , 1768:30-38 (2007)
43. Ramos, J., Lazaridis, T. “Energetic determinants of oligomeric state specificity in coiled coils”, J. Am. Chem. Soc. , 128:15499-15510 (2006)
42. Zhang, JM., Lazaridis, T. “Calculating the association free energy of transmembrane helices”, Biophys. J. , 91:1710-23 (2006)
41. Mottamal, M., Lazaridis, T. “Voltage-dependent energetics of alamethicin monomers in the membrane”, Biophys. Chem. , 122:50-7 (2006)
40. Mihajlovic, M., Lazaridis, T. “Calculations of pH-dependent binding of proteins to biological membranes”, J. Phys. Chem. B , 110:3375-84 (2006)
39. Li, Z., Lazaridis, T. “Thermodynamics of buried water clusters at a protein-ligand binding interface”, J. Phys. Chem. B, 110:1464-75 (2006)
38. Madhusoodanan, M., Zhang, JM, Lazaridis, T., “Energetics of the native and nonnative states of the Glycophorin A transmembrane helix dimer”,Proteins, 62:996-1009 (2006)
37. Lazaridis, T., Mallik, B., Chen, Y. “Implicit Solvent Simulations of DPC Micelle Formation”, J. Phys. Chem. B , 109:15098-106 (2005)
36. Lazaridis, T. “Structural Determinants of Transmembrane Beta-Barrels”, J. Chem. Theory Comput., 1:716-22 (2005)
35. Madhusoodanan, M., Lazaridis, T. “The contribution of Ca…O hydrogen bonds to membrane protein stability depends on the position of the amide”, Biochemistry, 44:1607-13 (2005)
34. Li, Z., Lazaridis, T. “The effect of water displacement on binding thermodynamics: Concanavalin A”, J. Phys. Chem. B, 109:662-70 (2005)
33. Lazaridis, T. “Implicit solvent simulations of peptide interactions with
anionic lipid membranes”, Proteins, 58:518-27 (2005)
32. Li, Z., Lazaridis, T. “Thermodynamic contributions of the ordered water molecule in HIV-1 protease”, J. Am. Chem. Soc., 125:6636-7 (2003)
31. Lazaridis, T. “Effective energy function for proteins in lipid membranes”, Proteins, 52:176-192 (2003)
30. Madhusoodanan, M., Lazaridis, T. “Investigation of pathways for the low-pH conformational transition in Influenza Hemagglutinin”, Biophys. J., 84:1926-39 (2003)
29. Lazaridis, T., Karplus, M. “Thermodynamics of protein folding: A microscopic view”, Biophys. Chem. , 100:367-95 (2003)
28. Masunov, A., Lazaridis, T. “Potentials of mean force between ionizable aminoacid sidechains in aqueous solution”, J. Am. Chem. Soc. , 125:1722-30 (2003)
27. Lazaridis, T. “Binding affinity and specificity from computational studies”, Current Organic Chemistry, 6:1319-32 (2002)
26. Lazaridis, T., Masunov, A., Gandolfo, F. “Contributions to the binding free energy of ligands to avidin and streptavidin”, Proteins, 47:194-208 (2002)
25. Mallik, B, Masunov, A., Lazaridis, T. “Distance and exposure dependent effective dielectric function”, J. Comp. Chem., 23:1090-9 (2002)
24. Lazaridis, T. “Solvent size vs cohesive energy as the origin of hydrophobicity”, Acc. Chem. Res., 34:931-7 (2001)
23. Lazaridis, T., Karplus, M. “Microscopic basis of macromolecular thermodynamics”, in “Thermodynamics in Biology”, E. Di Cera (ed), Oxford University Press (2001), pp. 3-48.
22. Inuzuka, Y., Lazaridis, T. “On the unfolding of a-lytic protease and the role of the pro-region”, Proteins, 41:21-32 (2000)
21. Lazaridis, T. “Solvent reorganization energy and entropy in hydrophobic hydration”, J. Phys. Chem. B, 104:4964-79 (2000)
20. Lazaridis, T., Karplus, M. “Effective energy functions for protein structure prediction”, Curr. Opin. Struct. Biol., 10:139-145 (2000)
19. Dinner, A.R., Lazaridis, T., Karplus, M. “Understanding ß-hairpin formation”, Proc. Natl. Acad. Sci., 96:9068-73 (1999)
18. Lazaridis, T., Karplus, M. “Heat capacity and compactness of denatured proteins”, Biophysical Chemistry, 78:207-17 (1999)
17. Lazaridis, T., Karplus, M. “Discrimination of the native from misfolded protein models with an energy function including implicit solvation”, J. Mol. Biol., 288:477-487 (1999)
16. Lazaridis, T., Karplus, M. “Effective energy function for proteins in solution”, Proteins , 35:133-152 (1999)
15. Petrella, R.J., Lazaridis, T., Karplus, M. “Protein side chain conformer prediction: A test of the energy function”, Folding and Design, 3:353-77 (1998)
14. Lazaridis, T. “Inhomogeneous fluid approach to solvation thermodynamics. II. Application to simple fluids”, J. Phys. Chem. , 102:3542-3550 (1998)
13. Lazaridis, T. “Inhomogeneous fluid approach to solvation thermodynamics. I. Theory”, J. Phys. Chem. , 102:3531-3541 (1998)
12. Lazaridis, T., Karplus, M. “New View of Protein Folding reconciled with the Old through Multiple Unfolding Simulations”, Science, 278:1928-1931 (1997)
11. Lazaridis, T., Lee, I., Karplus, M. “Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin “, Protein Science, 6:2589-2605 (1997)
10. Lazaridis, T., Karplus, M. “Orientational correlations and entropy in liquid water”, Journal of Chemical Physics, 105:4294-4316 (1996)
9. Lazaridis, T., Archontis, G., Karplus, M. “The enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics”, Advances in Protein Chemistry, 47:231-306 (1995)
8. Lazaridis, T., Paulaitis, M.E. “Computational studies of conformational transitions in the active site of tosyl-a-chymotrypsin”, Journal of the American Chemical Society, 116:1546 (1994)
7. Lazaridis, T., Paulaitis, M.E. “The molecular origin of the large entropies of hydrophobic hydration”, in Statistical Mechanics, Protein Structure, and Protein-Substrate interactions, NATO ARW, Cargese/corsica, 1993
6. Lazaridis, T., Paulaitis, M.E. “Simulation studies of the hydration entropy of simple, hydrophobic solutes”, Journal of Physical Chemistry, 98:635 (1994)
5. Khare, R., Lazaridis, T., Paulaitis, M.E. “An internal coordinate approach to reaction path determination for conformational transitions in polymers “, Chemical Design Automation News , 8, August 1993
4. Lazaridis, T., Paulaitis, M.E. “Activity coefficients in dilute aqueous solutions from free energy simulations”, AICHE Journal, 39:1051 (1993)
3. Lazaridis, T., Paulaitis, M.E. response to comment by D.E. Smith, B.B. Laird, A.D.J. Haymet, Journal of Physical Chemistry , 97:5789 (1993)
2b. Lazaridis, T., Paulaitis, M.E. “Entropy of hydrophobic hydration: a new statistical mechanical formulation” 6th Intern. Conference on Fluid Properties and Phase Equilibria for Chemical Process Design, Cortina, Italy, 1992. Published in Fluid Phase Equilibria, 83:43 (1993)
2a. Lazaridis, T., Paulaitis, M.E. “Entropy of hydrophobic hydration: a new statistical mechanical formulation” Mater. Res. Soc. Symp. Proc. 278 (Computational methods in Materials Science), pp. 319-24
2. Lazaridis, T., Paulaitis, M.E. “Entropy of hydrophobic hydration: a new statistical mechanical formulation” Journal of Physical Chemistry, 96:3847 (1992)
1. Lazaridis, T., Tobias, D.J., Brooks, C.L.III, and Paulaitis, M.E. “Reaction paths and free energy profiles for conformational transitions: an internal coordinate approach”, Journal of Chemical Physics, 95:7612 (1991)