-
1
-
-
0036285985
-
Molecular dynamics simulations of biomolecules
-
Karplus, M. 2002. Molecular dynamics simulations of biomolecules. Acc. Chem. Res. 35:321-323.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 321-323
-
-
Karplus, M.1
-
3
-
-
0021472805
-
Structure and dynamics of ion transport through gramicidin A
-
Mackay, D. H. J., P. H. Berens, K. R. Wilson, and A. T. Hagler. 1984. Structure and dynamics of ion transport through gramicidin A. Biophys. J. 46:229-248.
-
(1984)
Biophys. J.
, vol.46
, pp. 229-248
-
-
Mackay, D.H.J.1
Berens, P.H.2
Wilson, K.R.3
Hagler, A.T.4
-
4
-
-
0028321565
-
Molecular dynamics simulations of the gramicidin channel
-
Roux, B., and M. Karplus. 1994. Molecular dynamics simulations of the gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 23:731-761.
-
(1994)
Annu. Rev. Biophys. Biomol. Struct.
, vol.23
, pp. 731-761
-
-
Roux, B.1
Karplus, M.2
-
5
-
-
0036280795
-
Computational studies of the gramicidin A channel
-
Roux, B. 2002. Computational studies of the gramicidin A channel. Acc. Chem. Res. 35:366-375.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 366-375
-
-
Roux, B.1
-
6
-
-
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
Chait, B.T.7
MacKinnon, R.8
-
7
-
-
7044224837
-
Computer simulations of membrane proteins
-
Ash, W. L., M. R. Zlomislic, E. O. Oloo, and D. P. Tieleman. 2004. Computer simulations of membrane proteins. Biochim. Biophys. Acta. 1666:158-189.
-
(2004)
Biochim. Biophys. Acta.
, vol.1666
, pp. 158-189
-
-
Ash, W.L.1
Zlomislic, M.R.2
Oloo, E.O.3
Tieleman, D.P.4
-
8
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Comm. 91:1-41.
-
(1995)
Comput. Phys. Comm.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
DeBolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
9
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fisher, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fisher, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
11
-
-
2942660061
-
Ionic permeation free energy in gramicidin: A semimicroscopic perspective
-
Dorman, V. L., and P. C. Jordan. 2004. Ionic permeation free energy in gramicidin: a semimicroscopic perspective. Biophys. J. 86:3529-3541.
-
(2004)
Biophys. J.
, vol.86
, pp. 3529-3541
-
-
Dorman, V.L.1
Jordan, P.C.2
-
12
-
-
0026471029
-
Molecular determinants of channel function
-
Andersen, O. S., and R. E. Koeppe. 1992. Molecular determinants of channel function. Physiol. Rev. 72:89-158.
-
(1992)
Physiol. Rev.
, vol.72
, pp. 89-158
-
-
Andersen, O.S.1
Koeppe, R.E.2
-
13
-
-
0027533833
-
The use of physical methods in determining gramicidin structure and function
-
Busath, D. D. 1993. The use of physical methods in determining gramicidin structure and function. Annu. Rev. Physiol. 55:473-501.
-
(1993)
Annu. Rev. Physiol.
, vol.55
, pp. 473-501
-
-
Busath, D.D.1
-
15
-
-
0027069552
-
Theoretical perspectives on ion-channel electrostatics: Continuum and microscopic approaches
-
Partenskii, M. B., and P. C. Jordan. 1992. Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches. Q. Rev. Biophys. 25:477-510.
-
(1992)
Q. Rev. Biophys.
, vol.25
, pp. 477-510
-
-
Partenskii, M.B.1
Jordan, P.C.2
-
16
-
-
0035705881
-
Simulation approaches to ion channel structure-function relationships
-
Tieleman, D. P., P. C. Biggin, G. R. Smith, and M. S. P. Sansom. 2001. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34:473-561.
-
(2001)
Q. Rev. Biophys.
, vol.34
, pp. 473-561
-
-
Tieleman, D.P.1
Biggin, P.C.2
Smith, G.R.3
Sansom, M.S.P.4
-
17
-
-
0036708445
-
Continuum electrostatics fails to describe ion permeation in the gramicidin channel
-
Edwards, S., B. Corry, S. Kuyucak, and S. H. Chung. 2002. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophys. J. 83:1348-1360.
-
(2002)
Biophys. J.
, vol.83
, pp. 1348-1360
-
-
Edwards, S.1
Corry, B.2
Kuyucak, S.3
Chung, S.H.4
-
18
-
-
0036708441
-
Trial by ordeal: Ionic free energies in gramicidin
-
Jordan, P. C. 2002. Trial by ordeal: ionic free energies in gramicidin. Biophys. J. 83:1235-1236.
-
(2002)
Biophys. J.
, vol.83
, pp. 1235-1236
-
-
Jordan, P.C.1
-
19
-
-
0030050164
-
A semimicroscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: The origin of cation selectivity
-
Dorman, V., M. B. Partenskii, and P. C. Jordan. 1996. A semimicroscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity. Biophys. J. 70:121-134.
-
(1996)
Biophys. J.
, vol.70
, pp. 121-134
-
-
Dorman, V.1
Partenskii, M.B.2
Jordan, P.C.3
-
20
-
-
0029731562
-
Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study
-
Roux, B. 1996. Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study. Biophys. J. 71:3177-3185.
-
(1996)
Biophys. J.
, vol.71
, pp. 3177-3185
-
-
Roux, B.1
-
21
-
-
0037380854
-
Gramicidin a as a test ground for molecular dynamics force fields
-
Allen, T. W., T. Bastug, S. Kuyucak, and S. H. Chung. 2003. Gramicidin A as a test ground for molecular dynamics force fields. Biophys. J. 84:2159-2168.
-
(2003)
Biophys. J.
, vol.84
, pp. 2159-2168
-
-
Allen, T.W.1
Bastug, T.2
Kuyucak, S.3
Chung, S.H.4
-
22
-
-
0347089020
-
Energetics of ion conduction through the gramicidin channel
-
Allen, T. W., O. S. Andersen, and B. Roux. 2004. Energetics of ion conduction through the gramicidin channel. Proc. Natl. Acad. Sci. USA. 101:117-122.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 117-122
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
23
-
-
0033010064
-
Modeling of ion channels
-
Levitt, D. G. 1999. Modeling of ion channels. J. Gen. Physiol. 113: 789-794.
-
(1999)
J. Gen. Physiol.
, vol.113
, pp. 789-794
-
-
Levitt, D.G.1
-
25
-
-
33646177412
-
Role of protein flexibility in ion permeation: A case study in gramicidin A
-
Bastug, T., A. Gray-Weale, S. M. Patra, and S. Kuyucak. 2006. Role of protein flexibility in ion permeation: a case study in gramicidin A. Biophys. J. 90:2285-2296.
-
(2006)
Biophys. J.
, vol.90
, pp. 2285-2296
-
-
Bastug, T.1
Gray-Weale, A.2
Patra, S.M.3
Kuyucak, S.4
-
27
-
-
0031574382
-
High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints
-
Ketchem, R. R., B. Roux, and T. A. Cross. 1997. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure. 5:1655-1669.
-
(1997)
Structure
, vol.5
, pp. 1655-1669
-
-
Ketchem, R.R.1
Roux, B.2
Cross, T.A.3
-
29
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
30
-
-
36449007836
-
Constant pressure molecular dynamics: The Langevin piston method
-
Feller, S., Y. Zhang, R. Pastor, and B. Brooks. 1995. Constant pressure molecular dynamics: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.1
Zhang, Y.2
Pastor, R.3
Brooks, B.4
-
31
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23:187-199.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
32
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S., D. Bouzida, R. H. Swensen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13:1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swensen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
33
-
-
0035277126
-
Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations
-
Souaille, M., and B. Roux. 2001. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput. Phys. Commun. 135:40-57.
-
(2001)
Comput. Phys. Commun.
, vol.135
, pp. 40-57
-
-
Souaille, M.1
Roux, B.2
-
34
-
-
0022522698
-
Interpretation of biological ion channel flux data - Reaction-rate versus continuum theory
-
Levitt, D. G. 1986. Interpretation of biological ion channel flux data - reaction-rate versus continuum theory. Annu. Rev. Biophys. Biophys. Chem. 15:29-57.
-
(1986)
Annu. Rev. Biophys. Biophys. Chem.
, vol.15
, pp. 29-57
-
-
Levitt, D.G.1
-
35
-
-
3142652094
-
Theoretical and computational models of biological ion channels
-
Roux, B., T. Allen, S. Bernèche, and W. Im. 2004. Theoretical and computational models of biological ion channels. Q. Rev. Biophys. 37:15-103.
-
(2004)
Q. Rev. Biophys.
, vol.37
, pp. 15-103
-
-
Roux, B.1
Allen, T.2
Bernèche, S.3
Im, W.4
-
36
-
-
0024578173
-
Free energy via molecular simulation: Applications to chemical and biomolecular systems
-
Beveridge, D. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
-
(1989)
Annu. Rev. Biophys. Biophys. Chem.
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
37
-
-
0003474751
-
-
Cambridge University Press, Cambridge, UK
-
Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1989. Numerical Recipes. Cambridge University Press, Cambridge, UK.
-
(1989)
Numerical Recipes
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vetterling, W.T.4
-
38
-
-
0000827461
-
Comparison of selectively polarizable force fields for ion-water-peptide interactions: Ion translocation in a gramicidin-like channel
-
Duca, K. A., and P. C. Jordan. 1998. Comparison of selectively polarizable force fields for ion-water-peptide interactions: ion translocation in a gramicidin-like channel. J. Phys. Chem. 102:9127-9138.
-
(1998)
J. Phys. Chem.
, vol.102
, pp. 9127-9138
-
-
Duca, K.A.1
Jordan, P.C.2
-
41
-
-
0025878348
-
Location of ion-binding sites in the gramicidin channel by x-ray diffraction
-
Olah, G. A., H. W. Huang, W. Liu, and Y. Wu. 1991. Location of ion-binding sites in the gramicidin channel by x-ray diffraction. J. Mol. Biol. 218:847-858.
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 847-858
-
-
Olah, G.A.1
Huang, H.W.2
Liu, W.3
Wu, Y.4
-
42
-
-
0035797933
-
Structures of gramicidin A, B and C incorporated into sodium dodecyl sulfate micelles
-
Townsley, L. E., A. W. Tucker, S. Sham, and J. F. Hinton. 2001. Structures of gramicidin A, B and C incorporated into sodium dodecyl sulfate micelles. Biochemistry. 40:11676-11686.
-
(2001)
Biochemistry
, vol.40
, pp. 11676-11686
-
-
Townsley, L.E.1
Tucker, A.W.2
Sham, S.3
Hinton, J.F.4
-
43
-
-
0029787815
-
Monovalent cation transport: Lack of structural deformation upon cation binding
-
Tian, F., K. C. Lee, W. Hu, and T. A. Cross. 1996. Monovalent cation transport: lack of structural deformation upon cation binding. Biochemistry. 35:11959-11966.
-
(1996)
Biochemistry
, vol.35
, pp. 11959-11966
-
-
Tian, F.1
Lee, K.C.2
Hu, W.3
Cross, T.A.4
-
44
-
-
0033525064
-
Cation transport: An example of structural based selectivity
-
Tian, F., and T. A. Cross. 1999. Cation transport: an example of structural based selectivity. J. Mol. Biol. 285:1993-2003.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1993-2003
-
-
Tian, F.1
Cross, T.A.2
-
45
-
-
0017701531
-
Blocking of the gramicidin channel by divalent cations
-
Bamberg, E., and P. Laeuger. 1977. Blocking of the gramicidin channel by divalent cations. J. Membr. Biol. 35:351-375.
-
(1977)
J. Membr. Biol.
, vol.35
, pp. 351-375
-
-
Bamberg, E.1
Laeuger, P.2
-
46
-
-
0020827607
-
2+-gramicidin interaction and blocking effects on the ionic channel
-
2+-gramicidin interaction and blocking effects on the ionic channel. Biophys. Chem. 18:153-163.
-
(1983)
Biophys. Chem.
, vol.18
, pp. 153-163
-
-
Heitz, F.1
Gavach, C.2
-
47
-
-
0035132981
-
Mechanisms of permeation and selectivity in calcium channels
-
Corry, B., T. W. Allen, S. Kuyucak, and S. H. Chung. 2001. Mechanisms of permeation and selectivity in calcium channels. Biophys. J. 80:195-214.
-
(2001)
Biophys. J.
, vol.80
, pp. 195-214
-
-
Corry, B.1
Allen, T.W.2
Kuyucak, S.3
Chung, S.H.4
-
48
-
-
0026117352
-
The divalent cation-binding sites of gramicidin A transmembrane ion-channel
-
Golovanov, A. P., I. L. Barsukov, A. S. Arseniev, V. F. Bystrov, S. V. Sukhanov, and L. I. Barsukov. 1991. The divalent cation-binding sites of gramicidin A transmembrane ion-channel. Biopolymers. 31:425-434.
-
(1991)
Biopolymers
, vol.31
, pp. 425-434
-
-
Golovanov, A.P.1
Barsukov, I.L.2
Arseniev, A.S.3
Bystrov, V.F.4
Sukhanov, S.V.5
Barsukov, L.I.6
-
50
-
-
0033424652
-
Molecular models of water: Derivation and description
-
Wallqvist, A., and R. D. Mountain. 1999. Molecular models of water: derivation and description. Rev. Comput. Chem. 13:183-247.
-
(1999)
Rev. Comput. Chem.
, vol.13
, pp. 183-247
-
-
Wallqvist, A.1
Mountain, R.D.2
-
51
-
-
0142057630
-
Structural, electronic, and bonding properties of liquid water from first principles
-
Silvestrelli, P. L., and M. Parrinello. 1999. Structural, electronic, and bonding properties of liquid water from first principles. J. Chem. Phys. 111:3572-3580.
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 3572-3580
-
-
Silvestrelli, P.L.1
Parrinello, M.2
|