-
1
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, Gunsteren WF van, DiNola A, Haak JR (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
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
3
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure and constant temperature
-
Berger O, Edholm O, Jahnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure and constant temperature. Biophys J 72:2002-2013
-
(1997)
Biophys J
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
4
-
-
0011613265
-
Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane
-
Bernèche S, Nina M, Roux B (1998) Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J 75:1603-1618
-
(1998)
Biophys J
, vol.75
, pp. 1603-1618
-
-
Bernèche, S.1
Nina, M.2
Roux, B.3
-
5
-
-
0037007814
-
MD Simulations of a K channel model - Sensitivity to changes in ions, waters and membrane environment
-
in press
-
Capener CE, Sansom MSP (2002) MD Simulations of a K channel model - sensitivity to changes in ions, waters and membrane environment. J Phys Chem B (in press)
-
(2002)
J Phys Chem B
-
-
Capener, C.E.1
Sansom, M.S.P.2
-
6
-
-
0034123344
-
Homology modelling and molecular dynamics simulation studies of an inward rectifier potassium channel
-
Capener CE, Shrivastava IH, Ranatunga KM, Forrest LR, Smith GR, Sansom MSP (2000) Homology modelling and molecular dynamics simulation studies of an inward rectifier potassium channel. Biophys J 78:2929-2942
-
(2000)
Biophys J
, vol.78
, pp. 2929-2942
-
-
Capener, C.E.1
Shrivastava, I.H.2
Ranatunga, K.M.3
Forrest, L.R.4
Smith, G.R.5
Sansom, M.S.P.6
-
7
-
-
0035112130
-
Combined Monte Carlo and molecular dynamics simulation of hydrated lipid-cholesterol lipid bilayers at low cholesterol concentration
-
Chiu SW, Jacobson KA, Scott HL (2001) Combined Monte Carlo and molecular dynamics simulation of hydrated lipid-cholesterol lipid bilayers at low cholesterol concentration. Biophys J 80:1104-1114
-
(2001)
Biophys J
, vol.80
, pp. 1104-1114
-
-
Chiu, S.W.1
Jacobson, K.A.2
Scott, H.L.3
-
8
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
9
-
-
0032478818
-
+ conduction and selectivity
-
+ conduction and selectivity. Science 280:69-77
-
(1998)
Science
, vol.280
, pp. 69-77
-
-
Doyle, D.A.1
Cabral, J.M.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Cahit, B.T.7
MacKinnon, R.8
-
10
-
-
0032614136
-
Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities
-
Feller SE, Pastor RW (1999) Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities. J Chem Phys 111:1281-1287
-
(1999)
J Chem Phys
, vol.111
, pp. 1281-1287
-
-
Feller, S.E.1
Pastor, R.W.2
-
11
-
-
0032545324
-
Siderophore-mediated iron transport: Crystal structure of FhuA with bound lipopolysaccharide
-
Ferguson AD, Hofmann E, Coulton JW, Diederichs K, Welte W (1998) Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. Science 282:2215-2220
-
(1998)
Science
, vol.282
, pp. 2215-2220
-
-
Ferguson, A.D.1
Hofmann, E.2
Coulton, J.W.3
Diederichs, K.4
Welte, W.5
-
13
-
-
0032992048
-
Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer
-
Forrest LR, Tieleman DP, Sansom MSP (1999) Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer. Biophys J 76:1886-1896
-
(1999)
Biophys J
, vol.76
, pp. 1886-1896
-
-
Forrest, L.R.1
Tieleman, D.P.2
Sansom, M.S.P.3
-
14
-
-
0342419447
-
Single lipid diffusion in Langmuir monolayers
-
Forstner MB, Käs J, Martin D (2000) Single lipid diffusion in Langmuir monolayers. Langmuir 17:567-570
-
(2000)
Langmuir
, vol.17
, pp. 567-570
-
-
Forstner, M.B.1
Käs, J.2
Martin, D.3
-
15
-
-
0033761347
-
Structure of a glycerol-conducting channel and the basis of its selectivity
-
Fu D, Libson A, Miercke LJW, Weitzman C, Nollert P, Krucinski J, Stroud RM (2000) Structure of a glycerol-conducting channel and the basis of its selectivity. Science 290:481-486
-
(2000)
Science
, vol.290
, pp. 481-486
-
-
Fu, D.1
Libson, A.2
Miercke, L.J.W.3
Weitzman, C.4
Nollert, P.5
Krucinski, J.6
Stroud, R.M.7
-
16
-
-
0035252652
-
Probing the interface between membrane proteins and membrane lipids by X-ray crystallography
-
Fyfe PK, McAuley KE, Roszak AW, Isaacs NW, Codgell RJ, Jones MR (2001) Probing the interface between membrane proteins and membrane lipids by X-ray crystallography. Trends Biochem Sci 26:106-112
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 106-112
-
-
Fyfe, P.K.1
McAuley, K.E.2
Roszak, A.W.3
Isaacs, N.W.4
Codgell, R.J.5
Jones, M.R.6
-
18
-
-
0035918313
-
The TXP motif in the second transmembrane helix of CCR5 - A structural determinant of chemokine-induced activation
-
Govaerts C, Blanpain C, Deupi X, Ballet S, Ballesteros JA, Wodak SJ, Vassart G, Pardo L, Parmentier M (2001) The TXP motif in the second transmembrane helix of CCR5 - a structural determinant of chemokine-induced activation. J Biol Chem 276:13217-13225
-
(2001)
J Biol Chem
, vol.276
, pp. 13217-13225
-
-
Govaerts, C.1
Blanpain, C.2
Deupi, X.3
Ballet, S.4
Ballesteros, J.A.5
Wodak, S.J.6
Vassart, G.7
Pardo, L.8
Parmentier, M.9
-
22
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
23
-
-
0033932839
-
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
-
Lindahl E, Edholm O (2000) Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J 79:426-433
-
(2000)
Biophys J
, vol.79
, pp. 426-433
-
-
Lindahl, E.1
Edholm, O.2
-
24
-
-
0034907678
-
Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa
-
Lins RD, Straatsma TP (2001) Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa. Biophys J 81:1037-1046
-
(2001)
Biophys J
, vol.81
, pp. 1037-1046
-
-
Lins, R.D.1
Straatsma, T.P.2
-
25
-
-
0032414254
-
Transmembrane signalling across the ligand-gated FhuA receptor: Crystal structures of free and ferrichrome-bound states reveal allosteric changes
-
Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch J, Moras D (1998) Transmembrane signalling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell 95:771-778
-
(1998)
Cell
, vol.95
, pp. 771-778
-
-
Locher, K.P.1
Rees, B.2
Koebnik, R.3
Mitschler, A.4
Moulinier, L.5
Rosenbusch, J.6
Moras, D.7
-
26
-
-
0030815133
-
Raster3D photorealistic molecular graphics
-
Merritt EA, Bacon DJ (1997) Raster3D photorealistic molecular graphics. Methods Enzymol 277:505-524
-
(1997)
Methods Enzymol
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
27
-
-
0034609808
-
Structural determinants of water permeation through aquaporin-1
-
Murata K, Mitsuoaka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407:599-605
-
(2000)
Nature
, vol.407
, pp. 599-605
-
-
Murata, K.1
Mitsuoaka, K.2
Hirai, T.3
Walz, T.4
Agre, P.5
Heymann, J.B.6
Engel, A.7
Fujiyoshi, Y.8
-
28
-
-
0000732609
-
GRASP: Graphical representation and analysis of surface properties
-
Nicholls A, Bharadwaj R, Honig B (1993) GRASP: graphical representation and analysis of surface properties. Biophys J 64:166-170
-
(1993)
Biophys J
, vol.64
, pp. 166-170
-
-
Nicholls, A.1
Bharadwaj, R.2
Honig, B.3
-
29
-
-
0033802790
-
Anchoring of a monotopic membrane protein: The binding of prostaglandin H2 synthase-I to the surface of a phospholipid bilayer
-
Nina M, Bernèche S, Roux B (2000) Anchoring of a monotopic membrane protein: the binding of prostaglandin H2 synthase-I to the surface of a phospholipid bilayer. Eur Biophys J 29:439-454
-
(2000)
Eur Biophys J
, vol.29
, pp. 439-454
-
-
Nina, M.1
Bernèche, S.2
Roux, B.3
-
32
-
-
0034703270
-
Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: Molecular dynamics calculations
-
Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB (2000a) Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J Mol Biol 302:727-746
-
(2000)
J Mol Biol
, vol.302
, pp. 727-746
-
-
Petrache, H.I.1
Grossfield, A.2
MacKenzie, K.R.3
Engelman, D.M.4
Woolf, T.B.5
-
34
-
-
0032705715
-
Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane
-
Randa HS, Forrest LR, Voth GA, Sansom MSP (1999) Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. Biophys J 77:2400-2410
-
(1999)
Biophys J
, vol.77
, pp. 2400-2410
-
-
Randa, H.S.1
Forrest, L.R.2
Voth, G.A.3
Sansom, M.S.P.4
-
35
-
-
0035852730
-
Visualization of a water-selective pore by electron crystallography in vitreous ice
-
Ren G, Reddy VS, Cheng A, Melnyk P, Mitra AK (2001) Visualization of a water-selective pore by electron crystallography in vitreous ice. Proc Natl Acad Sci USA 98:1398-1403
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 1398-1403
-
-
Ren, G.1
Reddy, V.S.2
Cheng, A.3
Melnyk, P.4
Mitra, A.K.5
-
37
-
-
0039179572
-
Ion channels, permeation and electrostatics: Insight into the function of KcsA
-
Roux B, Bernèche S, Im W (2000) Ion channels, permeation and electrostatics: insight into the function of KcsA. Biochemistry 39:13295-13306
-
(2000)
Biochemistry
, vol.39
, pp. 13295-13306
-
-
Roux, B.1
Bernèche, S.2
Im, W.3
-
38
-
-
0033747203
-
Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A (1-17) in dimyristoylphosphatidylcholine bilayers
-
Sankararamakrishnan R, Weinstein H (2000) Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A (1-17) in dimyristoylphosphatidylcholine bilayers. Biophys J 79:2331-2344
-
(2000)
Biophys J
, vol.79
, pp. 2331-2344
-
-
Sankararamakrishnan, R.1
Weinstein, H.2
-
39
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38:305-320
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
41
-
-
0035250628
-
Molecular dynamics simulations of a phospholipid-detergent mixture
-
Schneider MJ, Feller SE (2001) Molecular dynamics simulations of a phospholipid-detergent mixture. J Phys Chem B 105:1331-1337
-
(2001)
J Phys Chem B
, vol.105
, pp. 1331-1337
-
-
Schneider, M.J.1
Feller, S.E.2
-
42
-
-
0028841033
-
A prokaryotic potassium-ion channel with 2 predicted transmembrane segments from Steptomyces lividans
-
Schrempf H, Schmidt O, Kummerlein R, Hinnah S, Muller D, Betzler M, Steinkamp T, Wagner R (1995) A prokaryotic potassium-ion channel with 2 predicted transmembrane segments from Steptomyces lividans. EMBO J 14:5170-5178
-
(1995)
EMBO J
, vol.14
, pp. 5170-5178
-
-
Schrempf, H.1
Schmidt, O.2
Kummerlein, R.3
Hinnah, S.4
Muller, D.5
Betzler, M.6
Steinkamp, T.7
Wagner, R.8
-
43
-
-
0030966534
-
Transmembrane helix structure, dynamics, and interactions: Multi-nanosecond molecular dynamics simulations
-
Shen L, Bassolino D, Stouch T (1997) Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. Biophys J 73:3-20
-
(1997)
Biophys J
, vol.73
, pp. 3-20
-
-
Shen, L.1
Bassolino, D.2
Stouch, T.3
-
44
-
-
0034036372
-
Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer
-
Shrivastava IH, Sansom MSP (2000) Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys J 78:557-570
-
(2000)
Biophys J
, vol.78
, pp. 557-570
-
-
Shrivastava, I.H.1
Sansom, M.S.P.2
-
46
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
Smart OS, Neduvelil JG, Wang X, Wallace BA, Sansom MSP (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graphics 14:354-360
-
(1996)
J Mol Graphics
, vol.14
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
47
-
-
0032850757
-
Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations
-
Tang YZ, Chen WZ, Wang CX, Shi YY (1999) Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations. Eur Biophys J 28:478-488
-
(1999)
Eur Biophys J
, vol.28
, pp. 478-488
-
-
Tang, Y.Z.1
Chen, W.Z.2
Wang, C.X.3
Shi, Y.Y.4
-
49
-
-
0010383761
-
Theoretical studies of membrane models
-
Rijksuniversiteit Groningen, Groningen
-
Tieleman DP (1998) Theoretical studies of membrane models. Biophysical Chemistry, Rijksuniversiteit Groningen, Groningen, p 192
-
(1998)
Biophysical Chemistry
, pp. 192
-
-
Tieleman, D.P.1
-
50
-
-
0031860932
-
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer
-
Tieleman DP, Berendsen HJC (1998) A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J 74:2786-2801
-
(1998)
Biophys J
, vol.74
, pp. 2786-2801
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
-
51
-
-
0031438285
-
A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
-
Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270
-
(1997)
Biochim Biophys Acta
, vol.1331
, pp. 235-270
-
-
Tieleman, D.P.1
Marrink, S.J.2
Berendsen, H.J.C.3
-
52
-
-
0033035249
-
An alamethicin channel in a lipid bilayer: Molecular dynamics simulations
-
Tieleman DP, Berendsen HJC, Sansom MSP (1999a) An alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys J 76:1757-1769
-
(1999)
Biophys J
, vol.76
, pp. 1757-1769
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
53
-
-
0032998180
-
Surface binding of alamethicin stabilises its helical structure: Molecular dynamics simulations
-
Tieleman DP, Berendsen HJC, Sansom MSP (1999b) Surface binding of alamethicin stabilises its helical structure: molecular dynamics simulations. Biophys J 76:3186-3191
-
(1999)
Biophys J
, vol.76
, pp. 3186-3191
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
54
-
-
0035132984
-
Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces
-
Tieleman DP, Berendsen HJC, Sansom MSP (2001) Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. Biophys J 80:331-346
-
(2001)
Biophys J
, vol.80
, pp. 331-346
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
55
-
-
0035312897
-
Electrostatics calculations: Recent methodological advances and applications to membranes
-
Tobias DJ (2001) Electrostatics calculations: recent methodological advances and applications to membranes. Curr Opin Struct Biol 11:253-261
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 253-261
-
-
Tobias, D.J.1
-
57
-
-
0027515072
-
Molecular dynamics simulations of a lipid bilayer and of hexadecane: An investigation of membrane fluidity
-
Venable RM, Zhang Y, Hardy BJ, Pastor RW (1993) Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science 262:223-226
-
(1993)
Science
, vol.262
, pp. 223-226
-
-
Venable, R.M.1
Zhang, Y.2
Hardy, B.J.3
Pastor, R.W.4
-
58
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms
-
Wallin E, Heijne G von (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms. Protein Sci 7:1029-1038
-
(1998)
Protein Sci
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
59
-
-
0343005873
-
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation
-
Weber W, Hunenberger PH, McCammon JA (2000) Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B 104:3668-3675
-
(2000)
J Phys Chem B
, vol.104
, pp. 3668-3675
-
-
Weber, W.1
Hunenberger, P.H.2
McCammon, J.A.3
-
60
-
-
0028020035
-
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
-
Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci USA 91:11631-11635
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 11631-11635
-
-
Woolf, T.B.1
Roux, B.2
-
61
-
-
0030038849
-
Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin-A channel in a DMPC bilayer
-
Woolf TB, Roux B (1996) Structure, energetics, and dynamics of lipid-protein interactions: a molecular dynamics study of the gramicidin-A channel in a DMPC bilayer. Proteins Struct Funct Genet 24:92-114
-
(1996)
Proteins Struct Funct Genet
, vol.24
, pp. 92-114
-
-
Woolf, T.B.1
Roux, B.2
|