-
1
-
-
0029738872
-
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
-
DOI 10.1038/nsb1096-842
-
Wimley, W. C., and S. H. White. 1996. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3:842-848. (Pubitemid 26330634)
-
(1996)
Nature Structural Biology
, vol.3
, Issue.10
, pp. 842-848
-
-
Wimley, W.C.1
White, S.H.2
-
2
-
-
0032540234
-
Folding of -sheet membrane proteins: A hydrophobic hexapeptide model
-
DOI 10.1006/jmbi.1998.1640
-
Wimley, W. C., K. Hristova,, S. H. White. 1998. Folding of b-sheet membrane proteins: a hydrophobic hexapeptide model. J. Mol. Biol. 277:1091-1110. (Pubitemid 28190849)
-
(1998)
Journal of Molecular Biology
, vol.277
, Issue.5
, pp. 1091-1110
-
-
Wimley, W.C.1
Hristova, K.2
Ladokhin, A.S.3
Silvestro, L.4
Axelsen, P.H.5
White, S.H.6
-
3
-
-
0033613815
-
Folding of amphipathic -helices on membranes: Energetics of helix formation by melittin
-
DOI 10.1006/jmbi.1998.2346
-
Ladokhin, A. S., and S. H. White. 1999. Folding of amphipathic a-helices on membranes: energetics of helix formation by melittin. J. Mol. Biol. 285:1363-1369. (Pubitemid 29060439)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1363-1369
-
-
Ladokhin, A.S.1
White, S.H.2
-
4
-
-
0035812599
-
Energetics, stability, and prediction of transmembrane helices
-
DOI 10.1006/jmbi.2001.5008
-
Jayasinghe, S., K. Hristova, and S. H. White. 2001. Energetics, stability, and prediction of transmembrane helices. J. Mol. Biol. 312:927-934. (Pubitemid 32980315)
-
(2001)
Journal of Molecular Biology
, vol.312
, Issue.5
, pp. 927-934
-
-
Jayasinghe, S.1
Hristova, K.2
White, S.H.3
-
5
-
-
84855457273
-
Hydrogen-bond energetics drive helix formation in membrane interfaces
-
Almeida, P. F., A. S. Ladokhin, and S. H. White. 2012. Hydrogen-bond energetics drive helix formation in membrane interfaces. Biochim. Biophys. Acta. 1818:178-182.
-
(2012)
Biochim. Biophys. Acta
, vol.1818
, pp. 178-182
-
-
Almeida, P.F.1
Ladokhin, A.S.2
White, S.H.3
-
6
-
-
0019871670
-
Incorporation of melittin into phosphatidylcholine bilayers. Study of binding and conformational changes
-
Vogel, H. 1981. Incorporation of melittin into phosphatidylcholine bilayers. Study of binding and conformational changes. FEBS Lett. 134:37-42.
-
(1981)
FEBS Lett
, vol.134
, pp. 37-42
-
-
Vogel, H.1
-
7
-
-
0024328774
-
Interaction of melittin with phosphatidylcholine membranes. Binding isotherm and lipid head-group conformation
-
DOI 10.1021/bi00436a014
-
Kuchinka, E., and J. Seelig. 1989. Interaction of melittin with phosphatidylcholine membranes. Binding isotherm and lipid head-group conformation. Biochemistry. 28:4216-4221. (Pubitemid 19141622)
-
(1989)
Biochemistry
, vol.28
, Issue.10
, pp. 4216-4221
-
-
Kuchinka, E.1
Seelig, J.2
-
8
-
-
0025808271
-
Effective charge of melittin upon interaction with POPC vesicles
-
Beschiaschvili, G., and H.-D. Baeuerle. 1991. Effective charge of melittin upon interaction with POPC vesicles. Biochim. Biophys. Acta. 1068:195-200.
-
(1991)
Biochim. Biophys. Acta
, vol.1068
, pp. 195-200
-
-
Beschiaschvili, G.1
Baeuerle, H.-D.2
-
9
-
-
33751230498
-
Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations
-
DOI 10.1529/biophysj.106.084483
-
Benz, R. W., H. Nanda,, D. J. Tobias. 2006. Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations. Biophys. J. 91:3617-3629. (Pubitemid 44788305)
-
(2006)
Biophysical Journal
, vol.91
, Issue.10
, pp. 3617-3629
-
-
Benz, R.W.1
Nanda, H.2
Castro-Roman, F.3
White, S.H.4
Tobias, D.J.5
-
10
-
-
35348886062
-
Anton, a specialpurpose machine for molecular dynamics simulation
-
Shaw, D. E., M. M. Deneroff,, S. C. Wang. 2007. Anton, a specialpurpose machine for molecular dynamics simulation. Proceedings of the 34th Annual International Symposium for the Computer Architect. Comm. ACM. 51:91-97.
-
(2007)
Proceedings of the 34th Annual International Symposium for the Computer Architect. Comm. ACM
, vol.51
, pp. 91-97
-
-
Shaw, D.E.1
Deneroff, M.M.2
Wang, S.C.3
-
11
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
MacKerell, Jr., A. D., M. Feig, and C. L. Brooks, III. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1400-1415
-
-
MacKerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
12
-
-
77953377650
-
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
-
Klauda, J. B., R. M. Venable,, R. W. Pastor. 2010. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B. 114:7830-7843.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Pastor, R.W.3
-
13
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom forcefield on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236. (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
14
-
-
0035144532
-
Structure, location, and lipid perturbations of melittin at the membrane interface
-
Hristova, K., C. E. Dempsey, and S. H. White. 2001. Structure, location, and lipid perturbations of melittin at the membrane interface. Biophys. J. 80:801-811. (Pubitemid 32128331)
-
(2001)
Biophysical Journal
, vol.80
, Issue.2
, pp. 801-811
-
-
Hristova, K.1
Dempsey, C.E.2
White, S.H.3
-
15
-
-
0026746013
-
Helical structure and orientation of melittin in dispersed phospholipid membranes from amide exchange analysis in situ
-
DOI 10.1021/bi00163a003
-
Dempsey, C. E., and G. S. Butler. 1992. Helical structure and orientation of melittin in dispersed phospholipid membranes from amide exchange analysis in situ. Biochemistry. 31:11973-11977. (Pubitemid 23011338)
-
(1992)
Biochemistry
, vol.31
, Issue.48
, pp. 11973-11977
-
-
Dempsey, C.E.1
Butler, G.S.2
-
16
-
-
69249142709
-
Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: From kinetics to thermodynamics
-
Almeida, P. F., and A. Pokorny. 2009. Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: from kinetics to thermodynamics. Biochemistry. 48:8083-8093.
-
(2009)
Biochemistry
, vol.48
, pp. 8083-8093
-
-
Almeida, P.F.1
Pokorny, A.2
-
17
-
-
78650191386
-
CD spectroscopy of peptides and proteins bound to large unilamellar vesicles
-
Ladokhin, A. S., M. Fernández-Vidal, and S. H. White. 2010. CD spectroscopy of peptides and proteins bound to large unilamellar vesicles. J. Membr. Biol. 236:247-253.
-
(2010)
J. Membr. Biol
, vol.236
, pp. 247-253
-
-
Ladokhin, A.S.1
Fernández-Vidal, M.2
White, S.H.3
-
18
-
-
0022798958
-
The structure of melittin in membranes
-
Vogel, H., and F. Jahnig. 1986. The structure of melittin in membranes. Biophys. J. 50:573-582.
-
(1986)
Biophys. J
, vol.50
, pp. 573-582
-
-
Vogel, H.1
Jahnig, F.2
-
19
-
-
84864660053
-
Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations
-
Ulmschneider, J. P., J. C. Smith, E. Strandberg. 2012. Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys. J. 103:472-482.
-
(2012)
Biophys. J.
, vol.103
, pp. 472-482
-
-
Ulmschneider, J.P.1
Smith, J.C.2
Strandberg, E.3
-
20
-
-
22944460220
-
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
-
Shan, Y., J. L. Klepeis,, D. E. Shaw. 2005. Gaussian split Ewald: a fast Ewald mesh method for molecular simulation. J. Chem. Phys. 122:054101-054113.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 054101-054113
-
-
Shan, Y.1
Klepeis, J.L.2
Shaw, D.E.3
-
22
-
-
0029633168
-
GROMACS: A new message-passing parallel molecular dynamics implementation
-
Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS: a new message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91:43-56.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
Van Der Spoel, D.2
Van Drunen, R.3
-
23
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen,W. L., J. Chandrasekhar, M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
24
-
-
67949120080
-
United atom lipid parameters for combination with the optimized potentials for liquid simulations all-atom force fields
-
Ulmschneider, J. P., and M. B. Ulmschneider. 2009. United atom lipid parameters for combination with the optimized potentials for liquid simulations all-atom force fields. J. Chem. Theory Comput. 5:1803- 1813.
-
(2009)
J. Chem. Theory Comput
, vol.5
, pp. 1803-1813
-
-
Ulmschneider, J.P.1
Ulmschneider, M.B.2
-
25
-
-
0000388705
-
LINCS: A Linear Constraint Solver for molecular simulations
-
Hess, B., H. Bekker,, J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Biol. 18:1463-1472. (Pubitemid 127637344)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.12
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
26
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi, G., D. Donadio, and M. Parrinello. 2007. Canonical sampling through velocity rescaling. J. Chem. Phys. 126:014101.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
27
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma,, J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684- 3690.
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Haak, J.R.3
|