{"id":28,"date":"2016-09-03T01:35:25","date_gmt":"2016-09-03T01:35:25","guid":{"rendered":"http:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=28"},"modified":"2025-10-15T09:27:45","modified_gmt":"2025-10-15T09:27:45","slug":"publications","status":"publish","type":"page","link":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=28","title":{"rendered":"Publications"},"content":{"rendered":"<p>102. Rodriguez S.Y.V, Lazaridis T. \u201cSeeking the Membrane-Bound Structure of the Caveolin 8S Complex\u201d, J. Phys. Chem. B, 129, 7932-8 (2025) (<a href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/acs.jpcb.5c01585\">link)<\/a><\/p>\n<p>101. Dutta A., Lazaridis T. &#8220;Classical Models of Hydroxide for Proton Hopping Simulations&#8221;, J. Phys. Chem. B, 128, 12161-12170 (2024) <span style=\"font-size: inherit;\">(<\/span><a style=\"font-size: inherit;\" href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jpcb.4c05499\">link<\/a><span style=\"font-size: inherit;\">)<\/span><\/p>\n<p>100. Hwang W. et al.\u00a0 &#8220;CHARMM at 45: Enhancements in accessibility, functionality, and speed&#8221;, J. Phys. Chem. B, 128, 9976-10042 (2024) <span style=\"font-size: inherit;\">(<\/span><a style=\"font-size: inherit;\" href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jpcb.4c04100\">link<\/a><span style=\"font-size: inherit;\">)<\/span><\/p>\n<p>99. Maurer M., Lazaridis T. &#8220;Transmembrane \u03b2\u2011Barrel Models of \u03b1\u2011Synuclein Oligomers&#8221;, J. Chem. Inf. Model., 63, 7171-7179 (2023) (<a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jcim.3c00997\">link<\/a>)<\/p>\n<p>98. Rodriguez S.Y.V, Lazaridis T. &#8220;Simulations suggest a scaffolding mechanism of\u00a0membrane deformation by the caveolin 8S complex&#8221;, Biophys. J..,122, 4082-90\u00a0<span style=\"font-size: inherit;\">(2023) (<\/span><a style=\"font-size: inherit;\" href=\"https:\/\/www.cell.com\/biophysj\/fulltext\/S0006-3495(23)00585-4\">link<\/a><span style=\"font-size: inherit;\">)<\/span><\/p>\n<p>97. Maurer M., Lazaridis T. &#8220;Comparison of classical and ab initio simulations\u00a0of hydronium and aqueous proton transfer&#8221;, J. Chem. Phys.,127, 134506\u00a0<span style=\"font-size: inherit;\">(2023) (<\/span><a style=\"font-size: inherit;\" href=\"https:\/\/pubs.aip.org\/aip\/jcp\/article-abstract\/159\/13\/134506\/2914676\/Comparison-of-classical-and-ab-initio-simulations?redirectedFrom=fulltext\">link<\/a><span style=\"font-size: inherit;\">)<\/span><\/p>\n<p>96. Lazaridis T. &#8220;Proton Paths in Models of the Hv1 Proton Channel&#8221;, J. Phys. Chem. B,127, 7937\u22127945\u00a0<span style=\"font-size: inherit;\">(2023) (<\/span><a style=\"font-size: inherit;\" href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jpcb.3c03960?ref=pdf\">link<\/a><span style=\"font-size: inherit;\">)<\/span><\/p>\n<p>95. Dutta A., Sepehri A., Lazaridis T. &#8220;Putative Pore Structures of Amyloid \u03b2 25\u221235 in Lipid Bilayers&#8221;, Biochemistry, 62, 2549\u22122558 (2023) (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.biochem.3c00323?ref=pdf\">link<\/a>)<\/p>\n<p>94. Sepehri A., Lazaridis T. &#8220;Putative Structures of Membrane-Embedded Amyloid \u03b2 Oligomers&#8221;, ACS Chemical Neuroscience, 14:99-110 (2023) (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acschemneuro.2c00535?ref=pdf\">link<\/a>)<\/p>\n<p>93. Lazaridis T. &#8220;Molecular origins of asymmetric proton conduction in the influenza M2 channel&#8221;, Biophysical Journal, 122: 90-98 (2023) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349522009456\">link<\/a>)<\/p>\n<p>92. Lazaridis T., Sepehri A. &#8220;Amino acid deprotonation rates from classical force fields&#8221;, J Chem Phys, 157: 085101 (2022) (<a href=\"https:\/\/aip.scitation.org\/doi\/10.1063\/5.0101960\">link<\/a>)<\/p>\n<p>91. Sepehri A., Nepal B., Lazaridis T. &#8220;Distinct Modes of Action of IAPP Oligomers on Membranes&#8221;, J Chem Inf Model, 61:4645-4655 (2021) (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.1c00767\">link<\/a>)<\/p>\n<p>90. Nepal B., Sepehri A., Lazaridis T. &#8220;Mechanism of negative membrane curvature generation \u00a0by I-BAR domains&#8221;, Structure, 29:1440-1452 (2021) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0969212621002604\">link<\/a>)<\/p>\n<p>89. Sepehri A., Nepal B., Lazaridis T. &#8220;Lipid interactions of an actinoporin pore-forming oligomer&#8221;, Biophys. J. 120:1357-1366 (2021) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0006349521001521\">link<\/a>)<\/p>\n<p>88. Dixit M., Lazaridis T. &#8220;Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint&#8221;, J. Chem. Phys. 153: 054101 (2020) (<a href=\"https:\/\/aip.scitation.org\/doi\/full\/10.1063\/5.0016682\">link<\/a>)<\/p>\n<p>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., &#8220;The value of antimicrobial peptides &#8220;, The Lancet Inf. Dis. 20:E216-R230 (2020) (<a href=\"https:\/\/www.thelancet.com\/journals\/laninf\/article\/PIIS1473-3099(20)30327-3\/fulltext\">link<\/a>)<\/p>\n<p>86. Rodnin M.V., Vasquez-Montes V., Nepal B., Ladokhin A.S., Lazaridis T., &#8220;Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers&#8221;, J. Mem. Biol. 253:287-98 (2020) (<a href=\"https:\/\/link.springer.com\/article\/10.1007\/s00232-020-00124-3\">link<\/a>)<\/p>\n<p>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. &#8221; 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&#8221;, J. Comp. Bioph. Chem. 20:111-130 (2021) (<a href=\"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S2737416520420016\">link<\/a>)<\/p>\n<p>84. Nepal B., Sepehri A., Lazaridis T. &#8220;Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7&#8221;, Pro. Sci., 29:1473-85 (2020) (<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/pro.3851\">link<\/a>)<\/p>\n<p>83. Sepehri A., PeBenito L, Pino-Angeles A., Lazaridis T. &#8220;What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives&#8221;, Biophys. J., 118:1901-13 (2020) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349520302034\">link<\/a>)<\/p>\n<p>82. Pino-Angeles A., Lazaridis T. &#8220;Effects of peptide charge, orientation, and concentration on melittin transmembrane pores&#8221;, Biophysical J, 114:2865 (2018) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349518305812\">link<\/a>)<\/p>\n<p>81. Nepal B., Leveritt J. III, Lazaridis T. &#8220;Membrane curvature sensing by amphipathic helices: Insights from implicit membrane modeling&#8221;, Biophysical J, 114:2128 (2018) (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349518304065\">link<\/a>)<\/p>\n<p>80. Lazaridis T., Hummer G. &#8220;Classical Molecular Dynamics with Mobile Protons&#8221;, J. Chem. Inf. Mod, 57:2833-45 (2017) (<a href=\"http:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.7b00603\">link<\/a>)<\/p>\n<p>79. Lipkin R., Pino-Angeles A., Lazaridis T. &#8220;Transmembrane Pore Structures of beta-Hairpin Antimicrobial Peptides by All-Atom Simulations&#8221;, J. Phys. Chem. B, 121:9126-40 (2017) (<a href=\"http:\/\/pubs.acs.org\/doi\/10.1021\/acs.jpcb.7b06591\">link<\/a>)<\/p>\n<p>78. Lipkin R., Lazaridis T. &#8220;Computational studies of peptide-induced membrane pore formation&#8221;, Phil. Trans. R. Soc. B, 372:20160219 (2017) (<a href=\"http:\/\/rstb.royalsocietypublishing.org\/content\/372\/1726\/20160219.long\">link<\/a>)<\/p>\n<p>77. Lipkin R., Lazaridis T. &#8220;Computational prediction of the optimal oligomeric state for membrane-inserted b-barrels of protegrin-1 and related mutants&#8221;, J Pep Sci, 23:334-45 (2017) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/psc.2992\/full\">link<\/a>)<\/p>\n<p>76. Pino-Angeles A.,Leveritt J.M. III, Lazaridis T. &#8220;Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family&#8221;, PLOS Comp. Biol. 12:e1004570 (2016) (<a href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1004570\">link<\/a>)<\/p>\n<p>75. Versace R., Lazaridis T. &#8220;Modeling Protein-Micelle Systems in Implicit Water&#8221;, J. Phys. Chem. B, 119:8037-47 (2015) (<a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.5b00171\">link<\/a>)<br \/>\n74. Leveritt J.M. III, Pino-Angeles A., Lazaridis T. &#8220;The Structure of a Melittin-Stabilized Pore&#8221;, Biophys J, 108:2424-6 (2015) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349515003847\">link<\/a>)<\/p>\n<p>73. Lipkin R.B., Lazaridis T. &#8220;Implicit Membrane Investigation of the Stability of Antimicrobial Peptide beta-barrels and arcs&#8221;, J Mem Biol, 248:469-86 (2015) (<a href=\"http:\/\/link.springer.com\/article\/10.1007\/s00232-014-9759-4\">link<\/a>)<\/p>\n<p>72. Brice A., Lazaridis T. &#8220;Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR&#8221;, J. Phys. Chem. B, 118:4461-70 (2014) (<a href=\"http:\/\/pubs.acs.org\/doi\/full\/10.1021\/jp409412g\">link<\/a>)<\/p>\n<p>71. Lazaridis T., Versace R. &#8220;The treatment of solvent in multiscale biophysical modeling&#8221;, Isr. J. Chem., 54:1074-83 (2014) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/ijch.201400006\/abstract\">link<\/a>)<\/p>\n<p>70. Lazaridis T., Leveritt JM, PeBenito L. &#8220;Implicit membrane treatment of buried charged groups. Application to peptide translocation across lipid bilayers&#8221;, BBA Biomembranes, 1838:2149-59 (2014) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0005273614000170\">link<\/a>)<\/p>\n<p>69. Prieto L., He Y., Lazaridis T. &#8220;Protein arcs may form stable pores in membranes&#8221;, Biophys J, 106:154-161 (2014) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349513057500\">link<\/a>)<\/p>\n<p>68. Rahaman A., Lazaridis, T. &#8220;A thermodynamic approach to alamethicin pore formation&#8221;, BBA Biomembranes 1838:98 (2014) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0005273613003179\">link<\/a>) Erratum: <a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0005273614000145\">link<\/a><\/p>\n<p>67. He Y., Lazaridis, T. &#8220;Activity Determinants of Helical Antimicrobial Peptides: A Large-scale Computational Study&#8221;, PLOS One, 8(6): e66440 (2013) (<a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0066440\">link<\/a>)<\/p>\n<p>66. He Y., Prieto L., Lazaridis, T. &#8220;Modeling Peptide Binding To Anionic Membrane Pores&#8221;, J Comp Chem, 34:1463-75 (2013) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.23282\/abstract\">link<\/a>)<\/p>\n<p>65. Lazaridis, T., He Y., Prieto L. &#8220;Membrane interactions and pore formation by the antimicrobial peptide protegrin&#8221;, Biophysical J, 104:633-42 (2013) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349512051545\">link<\/a>)<\/p>\n<p>64. Zhan H., Lazaridis, T. &#8220;Inclusion of Lateral Pressure\/Curvature Stress Effects in Implicit Membrane Models&#8221;, Biophysical J, 104:643-54 (2013) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349512051351\">link<\/a>)<\/p>\n<p>63. Yuzlenko O., Lazaridis, T. &#8220;Membrane protein native state discrimination by implicit membrane models&#8221;, J Comp Chem, 34:731-8 (2013) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.23189\/abstract\">link<\/a>)<\/p>\n<p>62. Lazaridis, T. &#8220;The hydrophobic effect&#8221;, in Encyclopedia of Life Sciences, Wiley, (2013) (<a href=\"http:\/\/www.els.net\/WileyCDA\/ElsArticle\/refId-a0002974.html\">link<\/a>)<\/p>\n<p>61. Mihajlovic, M., Lazaridis, T. &#8220;Charge Distribution and Imperfect Amphipathicity Affect Pore Formation by Antimicrobial Peptides&#8221;, BBA-Biomembranes , 1818:1274-83 (2012) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S000527361200020X\">link<\/a>)<\/p>\n<p>60. Lazaridis, T. &#8220;Ligand and Receptor Conformational Energies, in Protein-ligand interactions (Gohlke, H., Ed.), Wiley (2012)<\/p>\n<p>59. Li, Z., Lazaridis, T. &#8220;Computing the thermodynamic contributions of interfacial water&#8221;, Methods in Molecular Biology, 819:393-404 (2012) (<a href=\"http:\/\/www.springer.com\/biomed\/pharmaceutical+science\/book\/978-1-61779-464-3\">link<\/a>)<\/p>\n<p>58. Zhan H., Lazaridis, T. &#8220;Influence of the membrane dipole potential on peptide binding to lipid bilayers&#8221;, Biophys Chem, 161:1-7 (2012) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0301462211002900\">link<\/a>)<\/p>\n<p>57. Yuzlenko O., Lazaridis, T. &#8220;Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface&#8221;, J Phys Chem B, 115:13674-84 (2011) (<a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/jp2052213\">link<\/a>)<\/p>\n<p>56. Madeo J., Mihajlovic M., Lazaridis T., Gunner M.R. &#8220;Slow Dissociation of a Charged Ligand: Analysis of the Primary Quinone QA Site of Photosynthetic Bacterial Reaction Centers&#8221;, J Am Chem Soc, 133:17375-85 (2011) (<a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/ja205811f\">link<\/a>)<\/p>\n<p>55. Ramos J., Lazaridis, T. &#8220;Computational analysis of residue contributions to coiled-coil topology&#8221;, Protein Science, 20:1845-55 (2011) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.718\/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+on+27+October+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance\">link<\/a>)<\/p>\n<p>54. Prieto L., Lazaridis, T. &#8220;Computational studies of colicin insertion into membranes: The closed state&#8221;, Proteins, 79:126-141 (2011) (<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.22866\/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+on+27+October+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance\">link<\/a>)<\/p>\n<p>53. Mihajlovic, M., Lazaridis, T. &#8220;Antimicrobial Peptides in Toroidal and Cylindrical Pores&#8221;, <i>BBA-Biomembranes<\/i> , 1798:1485-1493 (2010) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S000527361000129X\">link<\/a>)<\/p>\n<p>52. Mihajlovic, M., Lazaridis, T. &#8220;Antimicrobial peptides bind more strongly to membrane pores&#8221;, <i>BBA-Biomembranes<\/i> , 1798:1494-1502 (2010) (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0005273610000829\">link<\/a>)<\/p>\n<p>51. Brooks, BR. et al. &#8220;CHARMM: The Biomolecular Simulation Program&#8221;, <i>J. Comp. Chem.<\/i> , 30: 1545-1614 (2009)<\/p>\n<p>50. Zhang, JM., Lazaridis, T. &#8220;Transmembrane Helix Association Affinity Can Be Modulated by Flanking and Noninterfacial Residues&#8221;, <i>Biophys. J.<\/i> , 96:4418-27 (2009)<\/p>\n<p>49. Hajjar, E., Mihajlovic, M., Witko-Sarsat, V., Lazaridis, T., Reuter, N. &#8220;Computational prediction of the binding site of proteinase 3 to the plasma membrane&#8221;, <i>Proteins<\/i> , 71:1655-69 (2008)<\/p>\n<p>48. Mihajlovic, M., Lazaridis, T. &#8220;Membrane-bound structure and energetics of alpha-synuclein&#8221;, <i>Proteins<\/i> , 70:761-78 (2008)<\/p>\n<p>47. Mihajlovic, M., Lazaridis, T. &#8220;Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane&#8221;, <i>Prot. Sci.<\/i> , 16:2042-55 (2007)<\/p>\n<p>46. Li, Z., Lazaridis, T. &#8220;Water at biomolecular binding interfaces&#8221;, <i>Phys. Chem. Chem. Phys.<\/i> , 9:573-81 (2007)<\/p>\n<p>45. Sammalkorpi, M., Lazaridis, T. &#8220;Modeling a spin labeled fusion peptide in a membrane: Implications for the interpretation of EPR experiments&#8221;, <i>Biophys. J. <\/i> , 92:10-22 (2007)<\/p>\n<p>44. Sammalkorpi, M., Lazaridis, T. &#8220;Configuration of influenza hemagglutinin fusion peptide monomers and oligomers in membranes&#8221;, <i>BBA Biomembranes <\/i> , 1768:30-38 (2007)<\/p>\n<p>43. Ramos, J., Lazaridis, T. &#8220;Energetic determinants of oligomeric state specificity in coiled coils&#8221;, <i>J. Am. Chem. Soc.<\/i> , 128:15499-15510 (2006)<\/p>\n<p>42. Zhang, JM., Lazaridis, T. &#8220;Calculating the association free energy of transmembrane helices&#8221;, <i>Biophys. J.<\/i> , 91:1710-23 (2006)<\/p>\n<p>41. Mottamal, M., Lazaridis, T. &#8220;Voltage-dependent energetics of alamethicin monomers in the membrane&#8221;, <i>Biophys. Chem.<\/i> , 122:50-7 (2006)<\/p>\n<p>40. Mihajlovic, M., Lazaridis, T. &#8220;Calculations of pH-dependent binding of proteins to biological membranes&#8221;, <i>J. Phys. Chem. B<\/i> , 110:3375-84 (2006)<\/p>\n<p>39. Li, Z., Lazaridis, T. &#8220;Thermodynamics of buried water clusters at a protein-ligand binding interface&#8221;, <i>J. Phys. Chem. B<\/i>, 110:1464-75 (2006)<\/p>\n<p>38. Madhusoodanan, M., Zhang, JM, Lazaridis, T., &#8220;Energetics of the native and nonnative states of the Glycophorin A transmembrane helix dimer&#8221;,<i>Proteins<\/i>, 62:996-1009 (2006)<\/p>\n<p>37. Lazaridis, T., Mallik, B., Chen, Y. &#8220;Implicit Solvent Simulations of DPC Micelle Formation&#8221;, <i>J. Phys. Chem. B <\/i>, 109:15098-106 (2005)<\/p>\n<p>36. Lazaridis, T. &#8220;Structural Determinants of Transmembrane Beta-Barrels&#8221;, <i>J. Chem. Theory Comput.<\/i>, 1:716-22 (2005)<\/p>\n<p>35. Madhusoodanan, M., Lazaridis, T. &#8220;The contribution of Ca&#8230;O hydrogen bonds to membrane protein stability depends on the position of the amide&#8221;, <i>Biochemistry<\/i>, 44:1607-13 (2005)<\/p>\n<p>34. Li, Z., Lazaridis, T. &#8220;The effect of water displacement on binding thermodynamics: Concanavalin A&#8221;, <i>J. Phys. Chem. B<\/i>, 109:662-70 (2005)<\/p>\n<p>33. Lazaridis, T. &#8220;Implicit solvent simulations of peptide interactions with<br \/>\nanionic lipid membranes&#8221;, <i>Proteins<\/i>, 58:518-27 (2005)<\/p>\n<p>32. Li, Z., Lazaridis, T. &#8220;Thermodynamic contributions of the ordered water molecule in HIV-1 protease&#8221;, <i>J. Am. Chem. Soc.<\/i>, 125:6636-7 (2003)<\/p>\n<p>31. Lazaridis, T. &#8220;Effective energy function for proteins in lipid membranes&#8221;, <i>Proteins<\/i>, 52:176-192 (2003)<\/p>\n<p>30. Madhusoodanan, M., Lazaridis, T. &#8220;Investigation of pathways for the low-pH conformational transition in Influenza Hemagglutinin&#8221;, <i>Biophys. J.<\/i>, 84:1926-39 (2003)<\/p>\n<p>29. Lazaridis, T., Karplus, M. &#8220;Thermodynamics of protein folding: A microscopic view&#8221;, <i>Biophys. Chem. <\/i>, 100:367-95 (2003)<\/p>\n<p>28. Masunov, A., Lazaridis, T. &#8220;Potentials of mean force between ionizable aminoacid sidechains in aqueous solution&#8221;, <i>J. Am. Chem. Soc. <\/i>, 125:1722-30 (2003)<\/p>\n<p>27. Lazaridis, T. &#8220;Binding affinity and specificity from computational studies&#8221;, <i>Current Organic Chemistry<\/i>, 6:1319-32 (2002)<\/p>\n<p>26. Lazaridis, T., Masunov, A., Gandolfo, F. &#8220;Contributions to the binding free energy of ligands to avidin and streptavidin&#8221;, <i>Proteins<\/i>, 47:194-208 (2002)<\/p>\n<p>25. Mallik, B, Masunov, A., Lazaridis, T. &#8220;Distance and exposure dependent effective dielectric function&#8221;, <i>J. Comp. Chem.<\/i>, 23:1090-9 (2002)<\/p>\n<p>24. Lazaridis, T. &#8220;Solvent size vs cohesive energy as the origin of hydrophobicity&#8221;, <i>Acc. Chem. Res.<\/i>, 34:931-7 (2001)<\/p>\n<p>23. Lazaridis, T., Karplus, M. &#8220;Microscopic basis of macromolecular thermodynamics&#8221;, in &#8220;Thermodynamics in Biology&#8221;, E. Di Cera (ed), Oxford University Press (2001), pp. 3-48.<\/p>\n<p>22. Inuzuka, Y., Lazaridis, T. &#8220;On the unfolding of a-lytic protease and the role of the pro-region&#8221;, <i>Proteins<\/i>, 41:21-32 (2000)<\/p>\n<p>21. Lazaridis, T. &#8220;Solvent reorganization energy and entropy in hydrophobic hydration&#8221;, <i>J. Phys. Chem. B<\/i>, 104:4964-79 (2000)<\/p>\n<p>20. Lazaridis, T., Karplus, M. &#8220;Effective energy functions for protein structure prediction&#8221;, <i>Curr. Opin. Struct. Biol.<\/i>, 10:139-145 (2000)<\/p>\n<p>19. Dinner, A.R., Lazaridis, T., Karplus, M. &#8220;Understanding \u00df-hairpin formation&#8221;, <i>Proc. Natl. Acad. Sci.<\/i>, 96:9068-73 (1999)<\/p>\n<p>18. Lazaridis, T., Karplus, M. &#8220;Heat capacity and compactness of denatured proteins&#8221;, <i>Biophysical Chemistry<\/i>, 78:207-17 (1999)<\/p>\n<p>17. Lazaridis, T., Karplus, M. &#8220;Discrimination of the native from misfolded protein models with an energy function including implicit solvation&#8221;, <i>J. Mol. Biol.<\/i>, 288:477-487 (1999)<\/p>\n<p>16. Lazaridis, T., Karplus, M. &#8220;Effective energy function for proteins in solution&#8221;, <i>Proteins <\/i>, 35:133-152 (1999)<\/p>\n<p>15. Petrella, R.J., Lazaridis, T., Karplus, M. &#8220;Protein side chain conformer prediction: A test of the energy function&#8221;, <i>Folding and Design<\/i>, 3:353-77 (1998)<\/p>\n<p>14. Lazaridis, T. &#8220;Inhomogeneous fluid approach to solvation thermodynamics. II. Application to simple fluids&#8221;, <i>J. Phys. Chem. <\/i>, 102:3542-3550 (1998)<\/p>\n<p>13. Lazaridis, T. &#8220;Inhomogeneous fluid approach to solvation thermodynamics. I. Theory&#8221;, <i>J. Phys. Chem. <\/i>, 102:3531-3541 (1998)<\/p>\n<p>12. Lazaridis, T., Karplus, M. &#8220;New View of Protein Folding reconciled with the Old through Multiple Unfolding Simulations&#8221;, <i>Science<\/i>, 278:1928-1931 (1997)<\/p>\n<p>11. Lazaridis, T., Lee, I., Karplus, M. &#8220;Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin &#8220;, <i>Protein Science<\/i>, 6:2589-2605 (1997)<\/p>\n<p>10. Lazaridis, T., Karplus, M. &#8220;Orientational correlations and entropy in liquid water&#8221;, <i>Journal of Chemical Physics<\/i>, 105:4294-4316 (1996)<\/p>\n<p>9. Lazaridis, T., Archontis, G., Karplus, M. &#8220;The enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics&#8221;, <i>Advances in Protein Chemistry<\/i>, 47:231-306 (1995)<\/p>\n<p>8. Lazaridis, T., Paulaitis, M.E. &#8220;Computational studies of conformational transitions in the active site of tosyl-a-chymotrypsin&#8221;, <i>Journal of the American Chemical Society<\/i>, 116:1546 (1994)<\/p>\n<p>7. Lazaridis, T., Paulaitis, M.E. &#8220;The molecular origin of the large entropies of hydrophobic hydration&#8221;, in Statistical Mechanics, Protein Structure, and Protein-Substrate interactions, NATO ARW, Cargese\/corsica, 1993<\/p>\n<p>6. Lazaridis, T., Paulaitis, M.E. &#8220;Simulation studies of the hydration entropy of simple, hydrophobic solutes&#8221;, <i>Journal of Physical Chemistry<\/i>, 98:635 (1994)<\/p>\n<p>5. Khare, R., Lazaridis, T., Paulaitis, M.E. &#8220;An internal coordinate approach to reaction path determination for conformational transitions in polymers &#8220;, <i>Chemical Design Automation News <\/i>, 8, August 1993<\/p>\n<p>4. Lazaridis, T., Paulaitis, M.E. &#8220;Activity coefficients in dilute aqueous solutions from free energy simulations&#8221;, <i>AICHE Journal<\/i>, 39:1051 (1993)<\/p>\n<p>3. Lazaridis, T., Paulaitis, M.E. response to comment by D.E. Smith, B.B. Laird, A.D.J. Haymet, <i>Journal of Physical Chemistry <\/i>, 97:5789 (1993)<\/p>\n<p>2b. Lazaridis, T., Paulaitis, M.E. &#8220;Entropy of hydrophobic hydration: a new statistical mechanical formulation&#8221; 6th Intern. Conference on Fluid Properties and Phase Equilibria for Chemical Process Design, Cortina, Italy, 1992. Published in <i>Fluid Phase Equilibria, <\/i> 83:43 (1993)<\/p>\n<p>2a. Lazaridis, T., Paulaitis, M.E. &#8220;Entropy of hydrophobic hydration: a new statistical mechanical formulation&#8221; <i>Mater. Res. Soc. Symp. Proc. 278 <\/i>(Computational methods in Materials Science), pp. 319-24<\/p>\n<p>2. Lazaridis, T., Paulaitis, M.E. &#8220;Entropy of hydrophobic hydration: a new statistical mechanical formulation&#8221; <i>Journal of Physical Chemistry<\/i>, 96:3847 (1992)<\/p>\n<p>1. Lazaridis, T., Tobias, D.J., Brooks, C.L.III, and Paulaitis, M.E. &#8220;Reaction paths and free energy profiles for conformational transitions: an internal coordinate approach&#8221;, <i>Journal of Chemical Physics<\/i>, 95:7612 (1991)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>102. Rodriguez S.Y.V, Lazaridis T. \u201cSeeking the Membrane-Bound Structure of the Caveolin 8S Complex\u201d, J. Phys. Chem. B, 129, 7932-8 (2025) (link) 101. Dutta A., Lazaridis T. &#8220;Classical Models of Hydroxide for Proton Hopping Simulations&#8221;, J. Phys. Chem. B, 128, 12161-12170 (2024) (link) 100. Hwang W. et al.\u00a0 &#8220;CHARMM at 45: Enhancements in accessibility, functionality, <a href=\"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/?page_id=28\" rel=\"nofollow\"><span class=\"sr-only\">Read more about Publications<\/span>[&hellip;]<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-fullwidth.php","meta":{"footnotes":""},"class_list":["post-28","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/28","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=28"}],"version-history":[{"count":22,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/28\/revisions"}],"predecessor-version":[{"id":349,"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/28\/revisions\/349"}],"wp:attachment":[{"href":"https:\/\/lazaridisgroup.ccny.cuny.edu\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}