Themis Lazaridis to Molecular Dynamics Simulation
This is a "connection" page, showing publications Themis Lazaridis has written about Molecular Dynamics Simulation.
Connection Strength
6.425
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Pino-Angeles A, Lazaridis T. Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores. Biophys J. 2018 06 19; 114(12):2865-2874.
Score: 0.510
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Lazaridis T, Hummer G. Classical Molecular Dynamics with Mobile Protons. J Chem Inf Model. 2017 11 27; 57(11):2833-2845.
Score: 0.490
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Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted ?-barrels of protegrin-1 and related mutants. J Pept Sci. 2017 Apr; 23(4):334-345.
Score: 0.469
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Versace RE, Lazaridis T. Modeling Protein-Micelle Systems in Implicit Water. J Phys Chem B. 2015 Jun 25; 119(25):8037-47.
Score: 0.414
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Brice AR, 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. 2014 May 01; 118(17):4461-70.
Score: 0.382
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Prieto L, He Y, Lazaridis T. Protein arcs may form stable pores in lipid membranes. Biophys J. 2014 Jan 07; 106(1):154-61.
Score: 0.375
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta. 2014 Jan; 1838(1 Pt B):98-105.
Score: 0.367
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Lazaridis T, He Y, Prieto L. Membrane interactions and pore formation by the antimicrobial peptide protegrin. Biophys J. 2013 Feb 05; 104(3):633-42.
Score: 0.352
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Zhan H, Lazaridis T. Inclusion of lateral pressure/curvature stress effects in implicit membrane models. Biophys J. 2013 Feb 05; 104(3):643-54.
Score: 0.352
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Ramos J, Lazaridis T. Computational analysis of residue contributions to coiled-coil topology. Protein Sci. 2011 Nov; 20(11):1845-55.
Score: 0.320
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Prieto L, Lazaridis T. Computational studies of colicin insertion into membranes: the closed state. Proteins. 2011 Jan; 79(1):126-41.
Score: 0.300
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Vasquez Rodriguez SY, Lazaridis T. Seeking the Membrane-Bound Structure of the Caveolin 8S Complex. J Phys Chem B. 2025 Aug 07; 129(31):7932-7938.
Score: 0.209
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Dutta A, Sepehri A, Lazaridis T. Putative Pore Structures of Amyloid ? 25-35 in Lipid Bilayers. Biochemistry. 2023 09 05; 62(17):2549-2558.
Score: 0.182
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Sepehri A, Lazaridis T. Putative Structures of Membrane-Embedded Amyloid ? Oligomers. ACS Chem Neurosci. 2023 01 04; 14(1):99-110.
Score: 0.174
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Lazaridis T. Molecular origins of asymmetric proton conduction in the influenza M2 channel. Biophys J. 2023 01 03; 122(1):90-98.
Score: 0.173
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Dixit M, Lazaridis T. Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint. J Chem Phys. 2020 Aug 07; 153(5):054101.
Score: 0.148
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Nepal B, Sepehri A, Lazaridis T. Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7. Protein Sci. 2020 06; 29(6):1473-1485.
Score: 0.144
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci. 2017 Aug 05; 372(1726).
Score: 0.120
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Pino-Angeles A, Leveritt JM, Lazaridis T. Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family. PLoS Comput Biol. 2016 Jan; 12(1):e1004570.
Score: 0.108
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Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide ?-Barrels and Arcs. J Membr Biol. 2015 Jun; 248(3):469-86.
Score: 0.100
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta. 2014 May; 1838(5):1439-47.
Score: 0.096
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Lazaridis T, Leveritt JM, PeBenito L. Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers. Biochim Biophys Acta. 2014 Sep; 1838(9):2149-59.
Score: 0.094
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He Y, Lazaridis T. Activity determinants of helical antimicrobial peptides: a large-scale computational study. PLoS One. 2013; 8(6):e66440.
Score: 0.090
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Li Z, Lazaridis T. Computing the thermodynamic contributions of interfacial water. Methods Mol Biol. 2012; 819:393-404.
Score: 0.081
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Yuzlenko O, Lazaridis T. Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B. 2011 Nov 24; 115(46):13674-84.
Score: 0.081
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Zhan H, Lazaridis T. Influence of the membrane dipole potential on peptide binding to lipid bilayers. Biophys Chem. 2012 Feb; 161:1-7.
Score: 0.081
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Mihajlovic M, Lazaridis T. Antimicrobial peptides in toroidal and cylindrical pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1485-93.
Score: 0.072
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Mihajlovic M, Lazaridis T. Antimicrobial peptides bind more strongly to membrane pores. Biochim Biophys Acta. 2010 Aug; 1798(8):1494-502.
Score: 0.072
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Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, K?ser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, T?pfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B. 2024 Oct 17; 128(41):9976-10042.
Score: 0.049
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Madeo J, Mihajlovic M, Lazaridis T, Gunner MR. Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers. J Am Chem Soc. 2011 Nov 02; 133(43):17375-85.
Score: 0.020