-
1
-
-
0030729453
-
Efficient characterization of collective motions and inter-residue correlations in proteins by low-resolution simulations
-
Bahar, I., B. Erman, T. Haliloglu, and R. L. Jernigan. 1997a. Efficient characterization of collective motions and inter-residue correlations in proteins by low-resolution simulations. Biochemistry. 36:13512-13523.
-
(1997)
Biochemistry
, vol.36
, pp. 13512-13523
-
-
Bahar, I.1
Erman, B.2
Haliloglu, T.3
Jernigan, R.L.4
-
2
-
-
0030324869
-
Coordination geometry of nonbonded residues in globular proteins
-
Bahar, I., and R. L. Jernigan. 1996. Coordination geometry of nonbonded residues in globular proteins. Fold. Des. 1:357-370.
-
(1996)
Fold. Des.
, vol.1
, pp. 357-370
-
-
Bahar, I.1
Jernigan, R.L.2
-
3
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
Bahar, I., M. Kaplan, and R. L. Jernigan. 1997b. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29:292-308.
-
(1997)
Proteins
, vol.29
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
4
-
-
0029762032
-
Insertion and hairpin formation of membrane proteins: A Monte Carlo study
-
Baumgartner, A. 1996. Insertion and hairpin formation of membrane proteins: a Monte Carlo study. Biophys. J. 71:1248-1255.
-
(1996)
Biophys. J.
, vol.71
, pp. 1248-1255
-
-
Baumgartner, A.1
-
5
-
-
0026192274
-
Orientations of amphipathic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy
-
Bechinger, B., Y. Kim, L. E. Chirlian, J. Gesell, J. M. Neumann, M. Montal, J. Tomich, M. Zasloff, and S. J. Opella. 1991. Orientations of amphipathic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy. J. Biomol. NMR. 1:167-173.
-
(1991)
J. Biomol. NMR
, vol.1
, pp. 167-173
-
-
Bechinger, B.1
Kim, Y.2
Chirlian, L.E.3
Gesell, J.4
Neumann, J.M.5
Montal, M.6
Tomich, J.7
Zasloff, M.8
Opella, S.J.9
-
6
-
-
0029938187
-
Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes
-
Ben-Shaul, A., N. Ben-Tal, and B. Honig. 1996. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. Biophys. J. 71:130-137.
-
(1996)
Biophys. J.
, vol.71
, pp. 130-137
-
-
Ben-Shaul, A.1
Ben-Tal, N.2
Honig, B.3
-
7
-
-
0029669955
-
Free-energy determinants of α-helix insertion into lipid bilayers
-
Ben-Tal, N., A. Ben-Shaul, A. Nicholls, and B. Honig. 1996. Free-energy determinants of α-helix insertion into lipid bilayers. Biophys. J. 70: 1803-1812.
-
(1996)
Biophys. J.
, vol.70
, pp. 1803-1812
-
-
Ben-Tal, N.1
Ben-Shaul, A.2
Nicholls, A.3
Honig, B.4
-
8
-
-
0031022167
-
Simulation studies of alamethicin-bilayer interactions
-
Biggin, P. C., J. Breed, H. S. Son, and M. S. Sansom. 1997. Simulation studies of alamethicin-bilayer interactions. Biophys. J. 72:627-636.
-
(1997)
Biophys. J.
, vol.72
, pp. 627-636
-
-
Biggin, P.C.1
Breed, J.2
Son, H.S.3
Sansom, M.S.4
-
9
-
-
0037018915
-
Stability of an ion channel in lipid bilayers: Implicit solvent model calculations with gramicidin
-
Bransburg-Zabary, S., A. Kessel, M. Gutman, and N. Ben-Tal. 2002. Stability of an ion channel in lipid bilayers: Implicit solvent model calculations with gramicidin. Biochemistry. 41:6946-6954.
-
(2002)
Biochemistry
, vol.41
, pp. 6946-6954
-
-
Bransburg-Zabary, S.1
Kessel, A.2
Gutman, M.3
Ben-Tal, N.4
-
11
-
-
0036893269
-
Transmembrane helix predictions revisited
-
Chen, C. P., A. Kemytsky, and B. Rost. 2002. Transmembrane helix predictions revisited. Protein Sci. 11:2774-2791.
-
(2002)
Protein Sci.
, vol.11
, pp. 2774-2791
-
-
Chen, C.P.1
Kemytsky, A.2
Rost, B.3
-
12
-
-
0031679215
-
Effect of lipid characteristics on the structure of transmembrane proteins
-
Dan, N., and S. A. Safran. 1998. Effect of lipid characteristics on the structure of transmembrane proteins. Biophys. J. 75:1410-1414.
-
(1998)
Biophys. J.
, vol.75
, pp. 1410-1414
-
-
Dan, N.1
Safran, S.A.2
-
13
-
-
0032032107
-
IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies
-
Ducarme, P., M. Rahman, and R. Brasseur. 1998. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins. 30:357-371.
-
(1998)
Proteins
, vol.30
, pp. 357-371
-
-
Ducarme, P.1
Rahman, M.2
Brasseur, R.3
-
14
-
-
0032991265
-
A solvent model for simulations of peptides in bilayers. I. Membrane-promoting α-helix formation
-
Efremov, R. G., D. E. Nolde, G. Vergoten, and A. S. Arseniev. 1999a. A solvent model for simulations of peptides in bilayers. I. Membrane-promoting α-helix formation. Biophys. J. 76:2448-2459.
-
(1999)
Biophys. J.
, vol.76
, pp. 2448-2459
-
-
Efremov, R.G.1
Nolde, D.E.2
Vergoten, G.3
Arseniev, A.S.4
-
15
-
-
0032991267
-
A solvent model for simulations of peptides in bilayers. H. Membrane-spanning α-helices
-
Efremov, R. G., D. E. Nolde, G. Vergoten, and A. S. Arseniev. 1999b. A solvent model for simulations of peptides in bilayers. H. Membrane-spanning α-helices. Biophys. J. 76:2460-2471.
-
(1999)
Biophys. J.
, vol.76
, pp. 2460-2471
-
-
Efremov, R.G.1
Nolde, D.E.2
Vergoten, G.3
Arseniev, A.S.4
-
16
-
-
0036280738
-
Interaction of cardiotoxins with membranes: A molecular modeling study
-
Efremov, R. G., P. E. Volynsky, D. E. Nolde, P. V. Dubovskii, and A. S. Arseniev. 2002a. Interaction of cardiotoxins with membranes: a molecular modeling study. Biophys. J. 83:144-153.
-
(2002)
Biophys. J.
, vol.83
, pp. 144-153
-
-
Efremov, R.G.1
Volynsky, P.E.2
Nolde, D.E.3
Dubovskii, P.V.4
Arseniev, A.S.5
-
17
-
-
0037189917
-
Monte Carlo simulations of voltage-driven translocation of a signal sequence
-
Efremov, R. G., P. E. Volynsky, D. E. Nolde, A. van Dalen, B. de Kruijff, and A. S. Arseniev. 2002b. Monte Carlo simulations of voltage-driven translocation of a signal sequence. FEBS Lett. 526:97-100.
-
(2002)
FEBS Lett.
, vol.526
, pp. 97-100
-
-
Efremov, R.G.1
Volynsky, P.E.2
Nolde, D.E.3
Van Dalen, A.4
De Kruijff, B.5
Arseniev, A.S.6
-
18
-
-
0019464222
-
The spontaneous insertion of proteins into and across membranes: The helical hairpin hypothesis
-
Engelman, D. M., and T. A. Steitz. 1981. The spontaneous insertion of proteins into and across membranes: the helical hairpin hypothesis. Cell. 23:411-422.
-
(1981)
Cell
, vol.23
, pp. 411-422
-
-
Engelman, D.M.1
Steitz, T.A.2
-
19
-
-
0027362726
-
A molecular model for lipid-protein interaction in membranes: The role of hydrophobic mismatch
-
Fattal, D. R., and A. Ben-Shaul. 1993. A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. Biophys. J. 65:1795-1809.
-
(1993)
Biophys. J.
, vol.65
, pp. 1795-1809
-
-
Fattal, D.R.1
Ben-Shaul, A.2
-
21
-
-
0032525271
-
Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin
-
Haliloglu, T., and I. Bahar. 1999. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins. 31:271-281.
-
(1999)
Proteins
, vol.31
, pp. 271-281
-
-
Haliloglu, T.1
Bahar, I.2
-
22
-
-
11744314103
-
Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations
-
Hao, M. H., and H. A. Scheraga. 1995. Statistical thermodynamics of protein folding: comparison of a mean-field theory with Monte Carlo simulations. J. Chem. Phys. 102:1334-1348.
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 1334-1348
-
-
Hao, M.H.1
Scheraga, H.A.2
-
23
-
-
0025231220
-
Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels
-
Helfrich, P., and E. Jakobsson. 1990. Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophys. J. 57:1075-1084.
-
(1990)
Biophys. J.
, vol.57
, pp. 1075-1084
-
-
Helfrich, P.1
Jakobsson, E.2
-
24
-
-
0000176654
-
Stability of "salt bridges" in membrane proteins
-
Honig, B. H., and W. L. Hubbell. 1984. Stability of "salt bridges" in membrane proteins. Proc. Natl. Acad. Sci. USA. 81:5412-5416.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 5412-5416
-
-
Honig, B.H.1
Hubbell, W.L.2
-
25
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
26
-
-
0024558250
-
The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
-
Jacobs, R. E., and S. H. White. 1989. The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry. 28:3421-3437.
-
(1989)
Biochemistry
, vol.28
, pp. 3421-3437
-
-
Jacobs, R.E.1
White, S.H.2
-
27
-
-
35448950945
-
Free energy determinants of peptide association with lipid bilayers
-
S. A. Simon and T. J. McIntosh, editors. Academic Press, San Diego
-
Kessel, A., and N. Ben-Tal. 2002. Free energy determinants of peptide association with lipid bilayers. In Peptide-Lipid Interactions. Current Topics in Membranes. S. A. Simon and T. J. McIntosh, editors. Academic Press, San Diego.
-
(2002)
Peptide-Lipid Interactions. Current Topics in Membranes
-
-
Kessel, A.1
Ben-Tal, N.2
-
28
-
-
0034118188
-
Continuum solvent model calculations of alamethicin-membrane interactions: Thermodynamic aspects
-
Kessel, A., D. S. Cafiso, and N. Ben-Tal. 2000a. Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys. J. 78:571-583.
-
(2000)
Biophys. J.
, vol.78
, pp. 571-583
-
-
Kessel, A.1
Cafiso, D.S.2
Ben-Tal, N.3
-
29
-
-
0033747198
-
Calculations suggest a pathway for the transmembrane migration of a hydrophobic peptide
-
Kessel, A., K. Schulten, and N. Ben-Tal. 2000b. Calculations suggest a pathway for the transmembrane migration of a hydrophobic peptide. Biophys. J. 79:2322-2330.
-
(2000)
Biophys. J.
, vol.79
, pp. 2322-2330
-
-
Kessel, A.1
Schulten, K.2
Ben-Tal, N.3
-
30
-
-
0345281586
-
Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations
-
Kurt, N., and T. Haliloglu. 1999. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 37:454-464.
-
(1999)
Proteins
, vol.37
, pp. 454-464
-
-
Kurt, N.1
Haliloglu, T.2
-
31
-
-
0035029408
-
Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations
-
Kurt, N., and T. Haliloglu. 2001. Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations. J. Biomol. Struct. Dyn. 18:713-731.
-
(2001)
J. Biomol. Struct. Dyn.
, vol.18
, pp. 713-731
-
-
Kurt, N.1
Haliloglu, T.2
-
32
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
33
-
-
0033067113
-
Peptide-bilayer interactions: Simulations of dermaseptin B, an antimicrobial peptide
-
La Rocca, P., Y. Shai, and M. S. Sansom. 1999. Peptide-bilayer interactions: simulations of dermaseptin B, an antimicrobial peptide. Biophys. Chem. 76:145-159.
-
(1999)
Biophys. Chem.
, vol.76
, pp. 145-159
-
-
La Rocca, P.1
Shai, Y.2
Sansom, M.S.3
-
34
-
-
0033996292
-
Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles
-
Law, R. J., L. R. Forrest, K. M. Ranatunga, P. La Rocca, D. P. Tieleman, and M. S. Sansom. 2000. Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles. Proteins. 39:47-55.
-
(2000)
Proteins
, vol.39
, pp. 47-55
-
-
Law, R.J.1
Forrest, L.R.2
Ranatunga, K.M.3
La Rocca, P.4
Tieleman, D.P.5
Sansom, M.S.6
-
35
-
-
84985649741
-
Vibrational approach to the dynamics of an α-helix
-
Levy, R. M., and M. Karplus. 1979. Vibrational approach to the dynamics of an α-helix. Biopolymers. 18:2465-2495.
-
(1979)
Biopolymers
, vol.18
, pp. 2465-2495
-
-
Levy, R.M.1
Karplus, M.2
-
36
-
-
0000333671
-
On the theory of helix-coil transition in polypeptides
-
Lifson, S., and A. Roig. 1961. On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34:1963-1974.
-
(1961)
J. Chem. Phys.
, vol.34
, pp. 1963-1974
-
-
Lifson, S.1
Roig, A.2
-
37
-
-
0035451179
-
Computational study of lipid-destabilizing protein fragments: Towards a comprehensive view of tilted peptides
-
Lins, L., B. Charloteaux, A. Thomas, and R. Brasseur. 2001. Computational study of lipid-destabilizing protein fragments: towards a comprehensive view of tilted peptides. Proteins. 44:435-447.
-
(2001)
Proteins
, vol.44
, pp. 435-447
-
-
Lins, L.1
Charloteaux, B.2
Thomas, A.3
Brasseur, R.4
-
38
-
-
0036218972
-
A Monte Carlo study of peptide insertion into lipid bilayers: Equilibrium conformations and insertion mechanisms
-
Maddox, M. W., and M. L. Longo. 2002. A Monte Carlo study of peptide insertion into lipid bilayers: equilibrium conformations and insertion mechanisms. Biophys. J. 82:244-263.
-
(2002)
Biophys. J.
, vol.82
, pp. 244-263
-
-
Maddox, M.W.1
Longo, M.L.2
-
40
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. J. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.J.5
-
41
-
-
0027390459
-
Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model
-
Milik, M., and J. Skolnick. 1993. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins. 15: 10-25.
-
(1993)
Proteins
, vol.15
, pp. 10-25
-
-
Milik, M.1
Skolnick, J.2
-
42
-
-
0029099311
-
A Monte Carlo model of FD and PF1 coat proteins in lipid membranes
-
Milik, M., and J. Skolnick. 1995. A Monte Carlo model of FD and PF1 coat proteins in lipid membranes. Biophys. J. 69:1382-1386.
-
(1995)
Biophys. J.
, vol.69
, pp. 1382-1386
-
-
Milik, M.1
Skolnick, J.2
-
43
-
-
0021474573
-
Mattress model of lipid-protein interactions in membranes
-
Mouritsen, O. G., and M. Bloom. 1984. Mattress model of lipid-protein interactions in membranes. Biophys. J. 46:141-153.
-
(1984)
Biophys. J.
, vol.46
, pp. 141-153
-
-
Mouritsen, O.G.1
Bloom, M.2
-
45
-
-
0031895461
-
Energetics of inclusion-induced bilayer deformations
-
Nielsen, C., M. Goulian, and O. S. Andersen. 1998. Energetics of inclusion-induced bilayer deformations. Biophys. J. 74:1966-1983.
-
(1998)
Biophys. J.
, vol.74
, pp. 1966-1983
-
-
Nielsen, C.1
Goulian, M.2
Andersen, O.S.3
-
46
-
-
0032919444
-
Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy
-
Opella, S. J., F. M. Marassi, J. J. Gesell, A. P. Valente, Y. Kim, M. Oblatt-Montal, and M. Montal. 1999. Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy. Nat. Struct. Biol. 6:374-379.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 374-379
-
-
Opella, S.J.1
Marassi, F.M.2
Gesell, J.J.3
Valente, A.P.4
Kim, Y.5
Oblatt-Montal, M.6
Montal, M.7
-
48
-
-
0031996814
-
Membrane-mediated protein attraction. A Monte Carlo study
-
Sintes, T., and A. Baumgartner. 1998. Membrane-mediated protein attraction. A Monte Carlo study. Physica A. 249:571-575.
-
(1998)
Physica A
, vol.249
, pp. 571-575
-
-
Sintes, T.1
Baumgartner, A.2
-
49
-
-
0038767500
-
Monte Carlo approaches to the protein folding problem
-
Skolnick, J., and A. Kolinski. 1999. Monte Carlo approaches to the protein folding problem. Adv. Chem. Physics. 105:203-242.
-
(1999)
Adv. Chem. Physics
, vol.105
, pp. 203-242
-
-
Skolnick, J.1
Kolinski, A.2
-
50
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
White, S. H., and W. C. Wimley. 1999. Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomol. Struct. 28: 319-365.
-
(1999)
Annu. Rev. Biophys. Biomol. Struct.
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
51
-
-
0036681386
-
Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
-
Zhang, Y., D. Kihara, and J. Skolnick. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48:192-201.
-
(2002)
Proteins
, vol.48
, pp. 192-201
-
-
Zhang, Y.1
Kihara, D.2
Skolnick, J.3
-
52
-
-
0000668407
-
Theory of the phase transition between helix and random coil in polypeptide chains
-
Zimm, B. H., and J. K. Bragg. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Phys. Chem. 31:526-535.
-
(1959)
J. Phys. Chem.
, vol.31
, pp. 526-535
-
-
Zimm, B.H.1
Bragg, J.K.2
|