-
1
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle R (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.2
-
2
-
-
13444262028
-
Recognition of transmembrane helices by the endoplasmic reticulum translocon
-
DOI 10.1038/nature03216
-
Hessa T, et al. (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433:377-381. (Pubitemid 40203311)
-
(2005)
Nature
, vol.433
, Issue.7024
, pp. 377-381
-
-
Hessa, T.1
Kim, H.2
Bihlmaier, K.3
Lundin, C.4
Boekel, J.5
Andersson, H.6
Nilsson, I.7
White, S.H.8
Von Heijne, G.9
-
3
-
-
27244444569
-
Interface connections of a transmembrane voltage sensor
-
DOI 10.1073/pnas.0507618102
-
Freites J, Tobias D, von Heijne G, White S (2005) Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci USA 102:15059-15064. (Pubitemid 41513334)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.42
, pp. 15059-15064
-
-
Freites, J.A.1
Tobias, D.J.2
Von Heijne, G.3
White, S.H.4
-
5
-
-
34047151404
-
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
-
Jones D (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23:538-544.
-
(2007)
Bioinformatics
, vol.23
, pp. 538-544
-
-
Jones, D.1
-
6
-
-
34047240165
-
A generalized born implicit-membrane representation compared to experimental insertion free energies
-
DOI 10.1529/biophysj.106.081810
-
Ulmschneider M, Ulmschneider J, Sansom M, Di Nola A (2007) A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophys J 92:2338-2349. (Pubitemid 46536417)
-
(2007)
Biophysical Journal
, vol.92
, Issue.7
, pp. 2338-2349
-
-
Ulmschneider, M.B.1
Ulmschneider, J.P.2
Sansom, M.S.P.3
Di Nolay, A.4
-
7
-
-
44449083478
-
Prediction of membrane-protein topology from first principles
-
DOI 10.1073/pnas.0711151105
-
Bernsel A, et al. (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci USA 105:7177-7181. (Pubitemid 351754451)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.20
, pp. 7177-7181
-
-
Bernsel, A.1
Viklund, H.2
Falk, J.3
Lindahl, E.4
Von Heijne, G.5
Elofsson, A.6
-
8
-
-
4644356464
-
Membrane-protein integration and the role of the translocation channel
-
DOI 10.1016/j.tcb.2004.09.002, PII S096289240400234X
-
Rapoport T, Goder V, Heinrich S, Matlack K (2004) Membrane-protein integration and the role of the translocation channel. Trends Cell Biol 14:568-575. (Pubitemid 39296619)
-
(2004)
Trends in Cell Biology
, vol.14
, Issue.10
, pp. 568-575
-
-
Rapoport, T.A.1
Goder, V.2
Heinrich, S.U.3
Matlack, K.E.S.4
-
9
-
-
33748602095
-
Molecular mechanisms of aquaporin biogenesis by the endoplasmic reticulum Sec61 translocon
-
DOI 10.1016/j.bbamem.2006.04.021, PII S0005273606001738, Auquporins
-
Pitonzo D, Skach W (2006) Molecular mechanisms of aquaporin biogenesis by the endoplasmic reticulum sec61 translocon. Biochim Biophys Acta 1758:976-988. (Pubitemid 44376752)
-
(2006)
Biochimica et Biophysica Acta - Biomembranes
, vol.1758
, Issue.8
, pp. 976-988
-
-
Pitonzo, D.1
Skach, W.R.2
-
10
-
-
23244456428
-
Crystal structure of a mammalian voltage-dependent Shaker family K+ channel
-
Long SB, Campbell EB, Mackinnon R (2005) Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309:897-903.
-
(2005)
Science
, vol.309
, pp. 897-903
-
-
Long, S.B.1
Campbell, E.B.2
Mackinnon, R.3
-
11
-
-
37249037182
-
Molecular code for transmembrane-helix recognition by the Sec61 translocon
-
DOI 10.1038/nature06387, PII NATURE06387
-
Hessa T, et al. (2007) Molecular code for transmembrane-helix recognition by the sec61 translocon. Nature 450:1026-1030. (Pubitemid 350273612)
-
(2007)
Nature
, vol.450
, Issue.7172
, pp. 1026-1030
-
-
Hessa, T.1
Meindl-Beinker, N.M.2
Bernsel, A.3
Kim, H.4
Sato, Y.5
Lerch-Bader, M.6
Nilsson, I.7
White, S.H.8
Von Heijne, G.9
-
12
-
-
0024286073
-
Influences of solvent water on protein folding: Free energies of solvation of cis and trans peptides are nearly identical
-
Radzicka A, Pedersen L, Wolfenden R (1988) Influences of solvent water on protein folding: Free energies of solvation of cis and trans peptides are nearly identical. Biochemistry 27:4538-4541.
-
(1988)
Biochemistry
, vol.27
, pp. 4538-4541
-
-
Radzicka, A.1
Pedersen, L.2
Wolfenden, R.3
-
13
-
-
33845424528
-
Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations
-
DOI 10.1529/biophysj.106.092767
-
Johansson ACV, Lindahl E (2006) Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophys J 91:4450-4463. (Pubitemid 44904231)
-
(2006)
Biophysical Journal
, vol.91
, Issue.12
, pp. 4450-4463
-
-
Johansson, A.C.V.1
Lindahl, E.2
-
14
-
-
43649094583
-
Distribution of amino acids in a lipid bilayer from computer simulations
-
MacCallum J, Bennett W, Tieleman D (2008) Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J 94:3393-3404.
-
(2008)
Biophys J
, vol.94
, pp. 3393-3404
-
-
MacCallum, J.1
Bennett, W.2
Tieleman, D.3
-
15
-
-
61749104028
-
Titratable amino acid solvation in lipid membranes as a function of protonation state
-
Johansson A, Lindahl E (2009) Titratable amino acid solvation in lipid membranes as a function of protonation state. J Phys Chem B 113:245-253.
-
(2009)
J Phys Chem B
, vol.113
, pp. 245-253
-
-
Johansson, A.1
Lindahl, E.2
-
16
-
-
50549097744
-
Assessing atomistic and coarse-grained force fields for protein-lipid interactions: The formidable challenge of an ionizable side chain in a membrane
-
Vorobyov I, Li L, Allen T (2008) Assessing atomistic and coarse-grained force fields for protein-lipid interactions: The formidable challenge of an ionizable side chain in a membrane. J Phys Chem B 112:9588-9602.
-
(2008)
J Phys Chem B
, vol.112
, pp. 9588-9602
-
-
Vorobyov, I.1
Li, L.2
Allen, T.3
-
17
-
-
66549128460
-
The role of lipid composition for insertion and stabilization of amino acids in membranes
-
Johansson A, Lindahl E (2009) The role of lipid composition for insertion and stabilization of amino acids in membranes. J Chem Phys 130:185101.
-
(2009)
J Chem Phys
, vol.130
, pp. 185101
-
-
Johansson, A.1
Lindahl, E.2
-
18
-
-
0015473745
-
Membrane proteins
-
Guidotti G (1972) Membrane proteins. Annu Rev Biochem 41:731-752.
-
(1972)
Annu Rev Biochem
, vol.41
, pp. 731-752
-
-
Guidotti, G.1
-
19
-
-
0347192985
-
X-ray structure of a protein-conducting channel
-
Van den Berg B, et al. (2004) X-ray structure of a protein-conducting channel. Nature 427:36-44.
-
(2004)
Nature
, vol.427
, pp. 36-44
-
-
Van Den Berg, B.1
-
20
-
-
48249095616
-
How translocons select transmembrane helices
-
White SH, von Heijne G (2008) How translocons select transmembrane helices. Annu Rev Biophys 37:23-42.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 23-42
-
-
White, S.H.1
Von Heijne, G.2
-
21
-
-
39749132236
-
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
-
Johansson AC, Lindahl E (2007) Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 70:1332-1344.
-
(2007)
Proteins
, vol.70
, pp. 1332-1344
-
-
Johansson, A.C.1
Lindahl, E.2
-
22
-
-
0000388705
-
LINCS: A Linear Constraint Solver for molecular simulations
-
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 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
-
23
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger O, Edholm O, Jähnig F (1997) Molecular dynamics simulation of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure and constant temperature. Biophys J 72:2002-2013. (Pubitemid 27184429)
-
(1997)
Biophysical Journal
, vol.72
, Issue.5
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
24
-
-
49549141675
-
Molecular dynamics of liquid n-butane near its boiling point
-
Ryckaert J, Bellemans A (1975) Molecular dynamics of liquid n-butane near its boiling point. Chem Phys Lett 30:123-125.
-
(1975)
Chem Phys Lett
, vol.30
, pp. 123-125
-
-
Ryckaert, J.1
Bellemans, A.2
-
25
-
-
0035828364
-
Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers
-
DOI 10.1063/1.1389469
-
Lindahl E, Edholm O (2001) Molecular dynamics simulation of nmr relaxation rates and slow dynamics in lipid bilayers. J Chem Phys 115:4938-4950. (Pubitemid 32902746)
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.10
, pp. 4938-4950
-
-
Lindahl, E.1
Edholm, O.2
-
26
-
-
21244462687
-
Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach
-
DOI 10.1529/biophysj.104.046821
-
Benz R, Castro-Roman F, Tobias D, White S (2005) Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach. Biophys J 88:805-817. (Pubitemid 40975920)
-
(2005)
Biophysical Journal
, vol.88
, Issue.2
, pp. 805-817
-
-
Benz, R.W.1
Castro-Roman, F.2
Tobias, D.J.3
White, S.H.4
-
27
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487. (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
28
-
-
33745630723
-
Membrane protein simulations with a united-atom lipid and all-atom protein model: Lipid-protein interactions, side chain transfer free energies and model proteins
-
DOI 10.1088/0953-8984/18/28/S07, PII S0953898406150286, S07
-
Tieleman D, MacCallum J, Ash W, Kandt C, Monticelli L (2006) Membrane protein simulation with an united atom lipid and alla atom protein model: Side chain transfer free energy and model proteins. J Phys Condens Matter 1221-S1234. (Pubitemid 43982969)
-
(2006)
Journal of Physics Condensed Matter
, vol.18
, Issue.28
-
-
Tieleman, D.P.1
MacCallum, J.L.2
Ash, W.L.3
Kandt, C.4
Xu, Z.5
Monticelli, L.6
-
29
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
ed Pullman B (Reidel, Dordrecht, The Netherlands)
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. Intermolecular Forces, ed Pullman B (Reidel, Dordrecht, The Netherlands), pp 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
30
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
DOI 10.1007/S008940100045
-
Lindahl E, Hess BA, van der Spoel D (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Model 7:306-317. (Pubitemid 36153547)
-
(2001)
Journal of Molecular Modeling
, vol.7
, Issue.8
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
31
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto S, Kollman PA (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952-962.
-
(1992)
J Comput Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
32
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8592.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8592
-
-
Essmann, U.1
|