Publications and reprints

80. Lazaridis T.,Hummer G. "Classical Molecular Dynamics with Mobile Protons", J. Chem. Inf. Mod, on the web (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) [PDF]

50. Zhang, JM., Lazaridis, T. "Transmembrane Helix Association Affinity Can Be Modulated by Flanking and Noninterfacial Residues", Biophys. J. , 96:4418-27 (2009) [PDF]

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) [PDF]

48. Mihajlovic, M., Lazaridis, T. "Membrane-bound structure and energetics of alpha-synuclein", Proteins , 70:761-78 (2008) [PDF]

47. Mihajlovic, M., Lazaridis, T. "Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane", Prot. Sci. , 16:2042-55 (2007) [PDF]

46. Li, Z., Lazaridis, T. "Water at biomolecular binding interfaces", Phys. Chem. Chem. Phys. , 9:573-81 (2007) [PDF]

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) [PDF]

44. Sammalkorpi, M., Lazaridis, T. "Configuration of influenza hemagglutinin fusion peptide monomers and oligomers in membranes", BBA Biomembranes , 1768:30-38 (2007) [PDF]

43. Ramos, J., Lazaridis, T. "Energetic determinants of oligomeric state specificity in coiled coils", J. Am. Chem. Soc. , 128:15499-15510 (2006) [PDF] [erratum] [suppl. info]

42. Zhang, JM., Lazaridis, T. "Calculating the association free energy of transmembrane helices", Biophys. J. , 91:1710-23 (2006) [PDF]

41. Mottamal, M., Lazaridis, T. "Voltage-dependent energetics of alamethicin monomers in the membrane", Biophys. Chem. , 122:50-7 (2006) [PDF]

40. Mihajlovic, M., Lazaridis, T. "Calculations of pH-dependent binding of proteins to biological membranes", J. Phys. Chem. B , 110:3375-84 (2006) [PDF]

39. Li, Z., Lazaridis, T. "Thermodynamics of buried water clusters at a protein-ligand binding interface", J. Phys. Chem. B, 110:1464-75 (2006) [PDF]

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) [PDF]

37. Lazaridis, T., Mallik, B., Chen, Y. "Implicit Solvent Simulations of DPC Micelle Formation", J. Phys. Chem. B , 109:15098-106 (2005) [PDF]

36. Lazaridis, T. "Structural Determinants of Transmembrane Beta-Barrels", J. Chem. Theory Comput., 1:716-22 (2005) [PDF]

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) [PDF]

34. Li, Z., Lazaridis, T. "The effect of water displacement on binding thermodynamics: Concanavalin A", J. Phys. Chem. B, 109:662-70 (2005) [PDF].

33. Lazaridis, T. "Implicit solvent simulations of peptide interactions with anionic lipid membranes", Proteins, 58:518-27 (2005) [PDF].

32. Li, Z., Lazaridis, T. "Thermodynamic contributions of the ordered water molecule in HIV-1 protease", J. Am. Chem. Soc., 125:6636-7 (2003) [PDF].

31. Lazaridis, T. "Effective energy function for proteins in lipid membranes", Proteins, 52:176-192 (2003) [PDF].

30. Madhusoodanan, M., Lazaridis, T. "Investigation of pathways for the low-pH conformational transition in Influenza Hemagglutinin", Biophys. J., 84:1926-39 (2003) [PDF].

29. Lazaridis, T., Karplus, M. "Thermodynamics of protein folding: A microscopic view", Biophys. Chem. , 100:367-95 (2003) [PDF].

28. Masunov, A., Lazaridis, T. "Potentials of mean force between ionizable aminoacid sidechains in aqueous solution", J. Am. Chem. Soc. , 125:1722-30 (2003) [PDF].

27. Lazaridis, T. "Binding affinity and specificity from computational studies", Current Organic Chemistry, 6:1319-32 (2002) [PDF].

26. Lazaridis, T., Masunov, A., Gandolfo, F. "Contributions to the binding free energy of ligands to avidin and streptavidin", Proteins, 47:194-208 (2002) [PDF].

25. Mallik, B, Masunov, A., Lazaridis, T. "Distance and exposure dependent effective dielectric function", J. Comp. Chem., 23:1090-9 (2002) [PDF].

24. Lazaridis, T. "Solvent size vs cohesive energy as the origin of hydrophobicity", Acc. Chem. Res., 34:931-7 (2001) [PDF].

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) [PDF].

21. Lazaridis, T. "Solvent reorganization energy and entropy in hydrophobic hydration", J. Phys. Chem. B, 104:4964-79 (2000) [PDF]

20. Lazaridis, T., Karplus, M. "Effective energy functions for protein structure prediction", Curr. Opin. Struct. Biol., 10:139-145 (2000) [PDF].

19. Dinner, A.R., Lazaridis, T., Karplus, M. "Understanding ß-hairpin formation", Proc. Natl. Acad. Sci., 96:9068-73 (1999) [PDF]

18. Lazaridis, T., Karplus, M. "Heat capacity and compactness of denatured proteins", Biophysical Chemistry, 78:207-17 (1999) [PDF].

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) [PDF]

16. Lazaridis, T., Karplus, M. "Effective energy function for proteins in solution", Proteins , 35:133-152 (1999) [PDF].

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) [PDF]

14. Lazaridis, T. "Inhomogeneous fluid approach to solvation thermodynamics. II. Application to simple fluids", J. Phys. Chem. , 102:3542-3550 (1998) [PDF]

13. Lazaridis, T. "Inhomogeneous fluid approach to solvation thermodynamics. I. Theory", J. Phys. Chem. , 102:3531-3541 (1998) [PDF]

12. Lazaridis, T., Karplus, M. "New View of Protein Folding reconciled with the Old through Multiple Unfolding Simulations", Science, 278:1928-1931 (1997) [PDF]

11. Lazaridis, T., Lee, I., Karplus, M. "Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin ", Protein Science, 6:2589-2605 (1997) [PDF].

10. Lazaridis, T., Karplus, M. "Orientational correlations and entropy in liquid water", Journal of Chemical Physics, 105:4294-4316 (1996) [PDF].

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) [PDF].

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)[PDF].

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) [PDF].

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) [PDF].

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) [PDF].