-
2
-
-
0037379781
-
Voltage-gated proton channels and other proton transfer pathways
-
Decoursey TE. Voltage-gated proton channels and other proton transfer pathways. Physiological Reviews 2003; 83:475-579.
-
(2003)
Physiological Reviews
, vol.83
, pp. 475-579
-
-
Decoursey, T.E.1
-
3
-
-
55649114895
-
Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method
-
Till MS, Essigke T, Becker T, Ullmann GM. Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method. The Journal of Physical Chemistry 2008; 112:13401-13410.
-
(2008)
The Journal of Physical Chemistry
, vol.112
, pp. 13401-13410
-
-
Till, M.S.1
Essigke, T.2
Becker, T.3
Ullmann, G.M.4
-
5
-
-
0017178344
-
Vectorial chemistry and the molecular mechanics of chemiosmotic coupling: power transmission by proticity
-
Mitchell P. Vectorial chemistry and the molecular mechanics of chemiosmotic coupling: power transmission by proticity. Biochem Soc Trans 1976; 4:399-430.
-
(1976)
Biochem Soc Trans
, vol.4
, pp. 399-430
-
-
Mitchell, P.1
-
6
-
-
0346735076
-
A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions
-
Bernal JD, Fowler RH. A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. Journal of Chemical Physics 1933; 1:515-548.
-
(1933)
Journal of Chemical Physics
, vol.1
, pp. 515-548
-
-
Bernal, J.D.1
Fowler, R.H.2
-
7
-
-
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
-
Perlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P. 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. Computer Physics Communications 1995; 91:1-41.
-
(1995)
Computer Physics Communications
, vol.91
, pp. 1-41
-
-
Perlman, 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
-
8
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell Jr. AD, Bashford D, Bellot M, Dunbrack Jr. RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher III WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 1998; 102(18):3586-3616.
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, 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
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
10
-
-
0036151669
-
Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations
-
Chung S-H, Allen TW, Kuyucak S. Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophysical Journal 2002; 82:628-645.
-
(2002)
Biophysical Journal
, vol.82
, pp. 628-645
-
-
Chung, S.-H.1
Allen, T.W.2
Kuyucak, S.3
-
11
-
-
0031030225
-
Permeation through an open channel: Poisson-Nernst-Planck theory of a synthetic ionic channel
-
Chen D, Lear J, Eisenberg B. Permeation through an open channel: Poisson-Nernst-Planck theory of a synthetic ionic channel. Biophysical Journal 1997; 72(1):97-116.
-
(1997)
Biophysical Journal
, vol.72
, Issue.1
, pp. 97-116
-
-
Chen, D.1
Lear, J.2
Eisenberg, B.3
-
12
-
-
0036708445
-
Continuum electrostatics fails to describe ion permeation in the gramicidin channel
-
September
-
Edwards S, Corry B, Kuyucak S, Chung S-H. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophysical Journal September 2002; 83:1348-1360.
-
(2002)
Biophysical Journal
, vol.83
, pp. 1348-1360
-
-
Edwards, S.1
Corry, B.2
Kuyucak, S.3
Chung, S.-H.4
-
13
-
-
0038440721
-
The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents
-
June
-
Mamonov AB, Coalson RD, Nitzan A, Kurnikova MG. The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents. Biophysical Journal June 2003; 84:3646-3661.
-
(2003)
Biophysical Journal
, vol.84
, pp. 3646-3661
-
-
Mamonov, A.B.1
Coalson, R.D.2
Nitzan, A.3
Kurnikova, M.G.4
-
14
-
-
0036225143
-
+ conduction in the single-file water chain of the gramicidin channel
-
+ conduction in the single-file water chain of the gramicidin channel. Biophysical Journal 2002; 82:2304-2316.
-
(2002)
Biophysical Journal
, vol.82
, pp. 2304-2316
-
-
Pomès, R.1
Roux, B.2
-
15
-
-
79251528566
-
MIBPB: a software package for electrostatic analysis
-
Chen D, Chen Z, Chen C, Geng WH, Wei GW. MIBPB: a software package for electrostatic analysis. Journal of Computational Chemistry 2011; 32:657-670.
-
(2011)
Journal of Computational Chemistry
, vol.32
, pp. 657-670
-
-
Chen, D.1
Chen, Z.2
Chen, C.3
Geng, W.H.4
Wei, G.W.5
-
16
-
-
34648817162
-
Treatment of charge singularities in implicit solvent models
-
Geng W, Yu S, Wei GW. Treatment of charge singularities in implicit solvent models. Journal of Chemical Physics 2007; 127:114106.
-
(2007)
Journal of Chemical Physics
, vol.127
, pp. 114106
-
-
Geng, W.1
Yu, S.2
Wei, G.W.3
-
17
-
-
34547352376
-
Treatment of geometric singularities in implicit solvent models
-
Yu SN, Geng WH, Wei GW. Treatment of geometric singularities in implicit solvent models. Journal of Chemical Physics 2007; 126:244108.
-
(2007)
Journal of Chemical Physics
, vol.126
, pp. 244108
-
-
Yu, S.N.1
Geng, W.H.2
Wei, G.W.3
-
18
-
-
31744448526
-
High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
-
Zhou YC, Zhao S, Feig M, Wei GW. High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources. Journal of Computational Physics 2006; 213(1):1-30.
-
(2006)
Journal of Computational Physics
, vol.213
, Issue.1
, pp. 1-30
-
-
Zhou, Y.C.1
Zhao, S.2
Feig, M.3
Wei, G.W.4
-
19
-
-
79955476670
-
Second-order Poisson-Nernst-Planck solver for ion transport
-
Zheng Q, Chen D, Wei GW. Second-order Poisson-Nernst-Planck solver for ion transport. Journal of Computational Physics 2011; 230:5239-5262.
-
(2011)
Journal of Computational Physics
, vol.230
, pp. 5239-5262
-
-
Zheng, Q.1
Chen, D.2
Wei, G.W.3
-
22
-
-
0030011088
-
+ translocation along the single-file water chain in the gramicidin A channel
-
+ translocation along the single-file water chain in the gramicidin A channel. Biophysical Journal 2002; 71:19-39.
-
(2002)
Biophysical Journal
, vol.71
, pp. 19-39
-
-
Pomès, R.1
Roux, B.2
-
23
-
-
12344277810
-
Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects
-
Braun-Sand S, Burykin A, Chu ZT, Warshel A. Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects. The Journal of Physical Chemistry B 2005; 109:583-592.
-
(2005)
The Journal of Physical Chemistry B
, vol.109
, pp. 583-592
-
-
Braun-Sand, S.1
Burykin, A.2
Chu, Z.T.3
Warshel, A.4
-
24
-
-
0033638375
-
A combined molecular dynamics and diffusion model of single proton conduction through gramicidin
-
Schumaker MF, Pomes R, Roux B. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophysical Journal 2000; 79:2840-2857.
-
(2000)
Biophysical Journal
, vol.79
, pp. 2840-2857
-
-
Schumaker, M.F.1
Pomes, R.2
Roux, B.3
-
25
-
-
84856396114
-
Quantum dynamics in continuum for proton transport I: basic formulation
-
Accepted
-
Chen D, Wei GW. Quantum dynamics in continuum for proton transport I: basic formulation. Communications in Computational Physics Accepted, 2011.
-
(2011)
Communications in Computational Physics
-
-
Chen, D.1
Wei, G.W.2
-
26
-
-
0017429069
-
Areas, volumes, packing, and protein structure
-
Richards FM. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering 1977; 6(1):151-176.
-
(1977)
Annual Review of Biophysics and Bioengineering
, vol.6
, Issue.1
, pp. 151-176
-
-
Richards, F.M.1
-
30
-
-
67650932053
-
Geometric and potential driving formation and evolution of biomolecular surfaces
-
Bates PW, Chen Z, Sun Y, Wei GW, Zhao S. Geometric and potential driving formation and evolution of biomolecular surfaces. Journal of Mathematical Biology 2009; 59:193-231.
-
(2009)
Journal of Mathematical Biology
, vol.59
, pp. 193-231
-
-
Bates, P.W.1
Chen, Z.2
Sun, Y.3
Wei, G.W.4
Zhao, S.5
-
31
-
-
77955229645
-
Differential geometry based multiscale models
-
Wei GW. Differential geometry based multiscale models. Bulletin of Mathematical Biology 2010; 72:1562-1622.
-
(2010)
Bulletin of Mathematical Biology
, vol.72
, pp. 1562-1622
-
-
Wei, G.W.1
-
32
-
-
77956414486
-
Differential geometry based solvation models I: Eulerian formulation
-
Chen Z, Baker NA, Wei GW. Differential geometry based solvation models I: Eulerian formulation. Journal of Computational Physics 2010; 229:8231-8258.
-
(2010)
Journal of Computational Physics
, vol.229
, pp. 8231-8258
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
33
-
-
81455139588
-
Differential geometry based solvation models II: Lagrangian formulation
-
DOI:10.1007/s00285-011-0402-z.
-
Chen Z, Baker NA, Wei GW. Differential geometry based solvation models II: Lagrangian formulation. Journal of Mathematical Biology 2011, DOI:10.1007/s00285-011-0402-z.
-
(2011)
Journal of Mathematical Biology
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
34
-
-
77952727732
-
The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?
-
Bothma JP, Gilmore JB, McKenzie RH. The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?New Journal of Physics 2010; 12:055002.
-
(2010)
New Journal of Physics
, vol.12
, pp. 055002
-
-
Bothma, J.P.1
Gilmore, J.B.2
McKenzie, R.H.3
-
35
-
-
1942504857
-
Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins
-
Cukier RI. Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins. Biochimica Et Biophysical Acta-Bioenergetics 2004; 1655:37-44.
-
(2004)
Biochimica Et Biophysical Acta-Bioenergetics
, vol.1655
, pp. 37-44
-
-
Cukier, R.I.1
-
36
-
-
77951621843
-
Modeling and simulation of electronic structure, material interface and random doping in nano-electronic devices
-
Chen D, Wei GW. Modeling and simulation of electronic structure, material interface and random doping in nano-electronic devices. Journal of Computational Physics 2010; 229:4431-4460.
-
(2010)
Journal of Computational Physics
, vol.229
, pp. 4431-4460
-
-
Chen, D.1
Wei, G.W.2
-
38
-
-
78149414200
-
Multiscale molecular dynamics using the matched interface and boundary method
-
Geng W, Wei GW. Multiscale molecular dynamics using the matched interface and boundary method. Journal of Computational Physics 2011; 230(2):435-457.
-
(2011)
Journal of Computational Physics
, vol.230
, Issue.2
, pp. 435-457
-
-
Geng, W.1
Wei, G.W.2
-
39
-
-
0030735981
-
Influence of the membrane potential on the free energy of an intrinsic protein
-
December
-
Roux B. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical JournalDecember 1997; 73:2980-2989.
-
(1997)
Biophysical Journal
, vol.73
, pp. 2980-2989
-
-
Roux, B.1
-
41
-
-
0001585447
-
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
-
Gilson MK, Davis ME, Luty BA, McCammon JA. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. Journal of Physical Chemistry 1993; 97(14):3591-3600.
-
(1993)
Journal of Physical Chemistry
, vol.97
, Issue.14
, pp. 3591-3600
-
-
Gilson, M.K.1
Davis, M.E.2
Luty, B.A.3
McCammon, J.A.4
-
42
-
-
3242886771
-
PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 2004; 32:W665-W667.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
43
-
-
0030040323
-
Reduced surface: an efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996; 38:305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
46
-
-
33745714399
-
Proton transfer in gramicidin water wires in phosphlipid bilayers: attenuation by phosphoethanolamine
-
Chernyshev A, Cukierman S. Proton transfer in gramicidin water wires in phosphlipid bilayers: attenuation by phosphoethanolamine. Biophysical Journal 1997; 91:580-587.
-
(1997)
Biophysical Journal
, vol.91
, pp. 580-587
-
-
Chernyshev, A.1
Cukierman, S.2
-
47
-
-
0030786782
-
Proton conduction in gramicidin A and in its dioxolane-linked dimer in different lipid bilayers
-
Cukierman S, Quigley EP, Crumrine DS. Proton conduction in gramicidin A and in its dioxolane-linked dimer in different lipid bilayers. Biophysical Journal 1997; 73:2489-2502.
-
(1997)
Biophysical Journal
, vol.73
, pp. 2489-2502
-
-
Cukierman, S.1
Quigley, E.P.2
Crumrine, D.S.3
|