-
1
-
-
1342309210
-
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
-
Altekar, G., S. Dwarkadas, J.P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics. 20:407-415. http://dx.doi.org/10.1093/bioinformatics/btg427
-
(2004)
Bioinformatics
, vol.20
, pp. 407-415
-
-
Altekar, G.1
Dwarkadas, S.2
Huelsenbeck, J.P.3
Ronquist, F.4
-
2
-
-
79956067240
-
Perspectives on: ion selectivity
-
Andersen, O.S. 2011. Perspectives on: ion selectivity. J. Gen. Physiol. 137:393-395. http://dx.doi.org/10.1085/jgp.201110651
-
(2011)
J. Gen. Physiol
, vol.137
, pp. 393-395
-
-
Andersen, O.S.1
-
3
-
-
0034690250
-
Ion permeation mechanism of the potassium channel
-
Åqvist, J., and V. Luzhkov. 2000. Ion permeation mechanism of the potassium channel. Nature. 404:881-884. http://dx.doi.org/ 10.1038/35009114
-
(2000)
Nature
, vol.404
, pp. 881-884
-
-
Åqvist, J.1
Luzhkov, V.2
-
4
-
-
0030031856
-
Use-dependent blockers and exit rate of the last ion from the multi-ion pore of a K+ channel
-
Baukrowitz, T., and G. Yellen. 1996. Use-dependent blockers and exit rate of the last ion from the multi-ion pore of a K+ channel. Science. 271:653-656. http://dx.doi.org/10.1126/science.271.5249.653
-
(1996)
Science
, vol.271
, pp. 653-656
-
-
Baukrowitz, T.1
Yellen, G.2
-
6
-
-
0035498860
-
Energetics of ion conduction through the K+ channel
-
Bernèche, S., and B. Roux. 2001. Energetics of ion conduction through the K+ channel. Nature. 414:73-77. http://dx.doi .org/10.1038/35102067
-
(2001)
Nature
, vol.414
, pp. 73-77
-
-
Bernèche, S.1
Roux, B.2
-
7
-
-
0015424492
-
Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons
-
Bezanilla, F., and C.M. Armstrong. 1972. Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons. J. Gen. Physiol. 60:588-608. http://dx .doi.org/10.1085/jgp.60.5.588
-
(1972)
J. Gen. Physiol
, vol.60
, pp. 588-608
-
-
Bezanilla, F.1
Armstrong, C.M.2
-
8
-
-
77955087369
-
Conformational dynamics in the selectivity filter of KcsA in response to potassium ion concentration
-
Bhate, M.P., B.J. Wylie, L. Tian, and A.E. McDermott. 2010. Conformational dynamics in the selectivity filter of KcsA in response to potassium ion concentration. J. Mol. Biol. 401:155-166. http://dx.doi.org/10.1016/j.jmb.2010.06.031
-
(2010)
J. Mol. Biol
, vol.401
, pp. 155-166
-
-
Bhate, M.P.1
Wylie, B.J.2
Tian, L.3
McDermott, A.E.4
-
9
-
-
78650972577
-
On the structural basis ofmodal gating behavior in K(+) channels
-
Chakrapani, S., J.F. Cordero-Morales, V. Jogini, A.C. Pan, D.M. Cortes, B. Roux, and E. Perozo. 2011. On the structural basis ofmodal gating behavior in K(+) channels. Nat. Struct. Mol. Biol. 18:67-74. http://dx.doi.org/10.1038/nsmb.1968
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 67-74
-
-
Chakrapani, S.1
Cordero-Morales, J.F.2
Jogini, V.3
Pan, A.C.4
Cortes, D.M.5
Roux, B.6
Perozo, E.7
-
10
-
-
79955124042
-
Mechanism for selectivity-inactivation coupling in KcsA potassium channels
-
Cheng, W.W., J.G. McCoy, A.N. Thompson, C.G. Nichols, and C.M. Nimigean. 2011. Mechanism for selectivity-inactivation coupling in KcsA potassium channels. Proc. Natl. Acad. Sci. USA. 108:5272-5277. http://dx.doi.org/10.1073/pnas.1014186108
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 5272-5277
-
-
Cheng, W.W.1
McCoy, J.G.2
Thompson, A.N.3
Nichols, C.G.4
Nimigean, C.M.5
-
11
-
-
0000410893
-
The principles of the stochastic interpretation of ion-channel mechanisms
-
B. Sakmann and E. Neher, editors. Springer, New York
-
Colquhoun, D., and A.G. Hawkes. 2009a. The principles of the stochastic interpretation of ion-channel mechanisms. In Single-Channel Recording. B. Sakmann and E. Neher, editors. Springer, New York. 397-482.
-
(2009)
Single-Channel Recording
, pp. 397-482
-
-
Colquhoun, D.1
Hawkes, A.G.2
-
12
-
-
0000410893
-
A Q-matrix cookbook: how to write only one program to calculate the single-channel and macroscopic predictions for any kinetic mechanism
-
B. Sakmann and E. Neher, editors. Springer, New York
-
Colquhoun, D., and A.G. Hawkes. 2009b. A Q-matrix cookbook: how to write only one program to calculate the single-channel and macroscopic predictions for any kinetic mechanism. In Single-Channel Recording. B. Sakmann and E. Neher, editors. Springer, New York. 589-633.
-
(2009)
Single-Channel Recording
, pp. 589-633
-
-
Colquhoun, D.1
Hawkes, A.G.2
-
13
-
-
33745041507
-
Molecular determinants of gating at the potassium-channel selectivity filter
-
Cordero-Morales, J.F., L.G. Cuello, Y. Zhao, V. Jogini, D.M. Cortes, B. Roux, and E. Perozo. 2006. Molecular determinants of gating at the potassium-channel selectivity filter. Nat. Struct. Mol. Biol. 13:311-318. http://dx.doi.org/10.1038/nsmb1069
-
(2006)
Nat. Struct. Mol. Biol
, vol.13
, pp. 311-318
-
-
Cordero-Morales, J.F.1
Cuello, L.G.2
Zhao, Y.3
Jogini, V.4
Cortes, D.M.5
Roux, B.6
Perozo, E.7
-
14
-
-
75749153312
-
Strict coupling between CFTR's catalytic cycle and gating of its Cl- ion pore revealed by distributions of open channel burst durations
-
- ion pore revealed by distributions of open channel burst durations. Proc. Natl. Acad. Sci. USA. 107:1241-1246. http://dx.doi.org/10.1073/ pnas.0911061107
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 1241-1246
-
-
Csanády, L.1
Vergani, P.2
Gadsby, D.C.3
-
15
-
-
79551660280
-
Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites
-
Derebe, M.G., D.B. Sauer, W. Zeng, A. Alam, N. Shi, and Y. Jiang. 2011. Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. Proc. Natl. Acad. Sci. USA. 108:598-602. http://dx.doi.org/10.1073/pnas.1013636108
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 598-602
-
-
Derebe, M.G.1
Sauer, D.B.2
Zeng, W.3
Alam, A.4
Shi, N.5
Jiang, Y.6
-
16
-
-
0032478818
-
The structure of the potassium channel: molecular basis of K+ conduction and selectivity
-
Doyle, D.A., J. Morais Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science. 280:69-77. http://dx.doi.org/10.1126/science.280.5360.69
-
(1998)
Science
, vol.280
, pp. 69-77
-
-
Doyle, D.A.1
Morais Cabral, J.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Chait, B.T.7
MacKinnon, R.8
-
17
-
-
77955550391
-
Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes
-
Egwolf, B., and B. Roux. 2010. Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J. Mol. Biol. 401:831-842. http://dx.doi.org/10.1016/j.jmb.2010.07.006
-
(2010)
J. Mol. Biol
, vol.401
, pp. 831-842
-
-
Egwolf, B.1
Roux, B.2
-
18
-
-
29144472228
-
Activationcoupled inactivation in the bacterial potassium channel KcsA
-
Gao, L., X. Mi, V. Paajanen, K. Wang, and Z. Fan. 2005. Activationcoupled inactivation in the bacterial potassium channel KcsA. Proc. Natl. Acad. Sci. USA. 102:17630-17635. http://dx.doi.org/10.1073/ pnas.0505158102
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 17630-17635
-
-
Gao, L.1
Mi, X.2
Paajanen, V.3
Wang, K.4
Fan, Z.5
-
19
-
-
0004012196
-
-
Chapman and Hall/CRC, Boca Raton, FL
-
Gelman, A. 2004. Bayesian Data Analysis. Chapman and Hall/CRC, Boca Raton, FL. 696 pp.
-
(2004)
Bayesian Data Analysis
, pp. 696
-
-
Gelman, A.1
-
20
-
-
61449197652
-
Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors
-
Gin, E., M. Falcke, L.E. Wagner, D.I. Yule, and J. Sneyd. 2009. Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors. J. Theor. Biol. 257:460-474. http://dx.doi .org/10.1016/j.jtbi.2008.12.020
-
(2009)
J. Theor. Biol
, vol.257
, pp. 460-474
-
-
Gin, E.1
Falcke, M.2
Wagner, L.E.3
Yule, D.I.4
Sneyd, J.5
-
21
-
-
77956889087
-
Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
-
Green, P.J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika. 82:711-732. http://dx.doi.org/10.1093/biomet/82.4.711
-
(1995)
Biometrika
, vol.82
, pp. 711-732
-
-
Green, P.J.1
-
22
-
-
0031594195
-
A permanent ion binding site located between two gates of the Shaker K+ channel
-
Harris, R.E., H.P. Larsson, and E.Y. Isacoff. 1998. A permanent ion binding site located between two gates of the Shaker K+ channel. Biophys. J. 74:1808-1820. http://dx.doi.org/10.1016/ S0006-3495(98)77891-9
-
(1998)
Biophys. J
, vol.74
, pp. 1808-1820
-
-
Harris, R.E.1
Larsson, H.P.2
Isacoff, E.Y.3
-
23
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
Hastings, W.K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109. http:// dx.doi.org/10.1093/biomet/57.1.97
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
24
-
-
0032875483
-
Single Streptomyces lividans K+ channels: functional asymmetries and sidedness of proton activation
-
Heginbotham, L., M. LeMasurier, L. Kolmakova-Partensky, and C. Miller. 1999. Single Streptomyces lividans K+ channels: functional asymmetries and sidedness of proton activation. J. Gen. Physiol. 114:551-560. http://dx.doi.org/10.1085/jgp.114.4.551
-
(1999)
J. Gen. Physiol
, vol.114
, pp. 551-560
-
-
Heginbotham, L.1
LeMasurier, M.2
Kolmakova-Partensky, L.3
Miller, C.4
-
25
-
-
0003443746
-
-
Third edition. Sinauer Associates, Sunderland, MA
-
Hille, B. 2001. Ion Channels of Excitable Membranes. Third edition. Sinauer Associates, Sunderland, MA. 814 pp.
-
(2001)
Ion Channels of Excitable Membranes
, pp. 814
-
-
Hille, B.1
-
26
-
-
0018117903
-
Potassium channels as multi-ion singlefile pores
-
Hille, B., and W. Schwarz. 1978. Potassium channels as multi-ion singlefile pores. J. Gen. Physiol. 72:409-442. http://dx.doi.org/10.1085/ jgp.72.4.409
-
(1978)
J. Gen. Physiol
, vol.72
, pp. 409-442
-
-
Hille, B.1
Schwarz, W.2
-
27
-
-
33748263658
-
The potassium permeability of a giant nerve fibre
-
Hodgkin, A.L., and R.D. Keynes. 1955. The potassium permeability of a giant nerve fibre. J. Physiol. 128:61-88.
-
(1955)
J. Physiol.
, vol.128
, pp. 61-88
-
-
Hodgkin, A.L.1
Keynes, R.D.2
-
30
-
-
0034855137
-
KcsA: it's a potassium channel
-
LeMasurier, M., L. Heginbotham, and C. Miller. 2001. KcsA: it's a potassium channel. J. Gen. Physiol. 118:303-314. http://dx.doi.org/ 10.1085/jgp.118.3.303
-
(2001)
J. Gen. Physiol
, vol.118
, pp. 303-314
-
-
LeMasurier, M.1
Heginbotham, L.2
Miller, C.3
-
31
-
-
0017866923
-
Electrostatic calculations for an ion channel I. Energy and potential profiles and interactions between ions
-
Levitt, D.G. 1978. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions. Biophys. J. 22:209-219. http://dx.doi.org/10.1016/S0006-3495 (78)85485-X
-
(1978)
Biophys. J
, vol.22
, pp. 209-219
-
-
Levitt, D.G.1
-
33
-
-
5744249209
-
Equations of state calculations by fast computing machines
-
Metropolis, N., A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1091. http://dx.doi.org/10.1063/ 1.1699114
-
(1953)
J. Chem. Phys
, vol.21
, pp. 1087-1091
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
34
-
-
0023369648
-
Trapping single ions inside single ion channels
-
Miller, C. 1987. Trapping single ions inside single ion channels. Biophys. J. 52:123-126. http://dx.doi.org/10.1016/S0006-3495 (87)83196-X
-
(1987)
Biophys. J.
, vol.52
, pp. 123-126
-
-
Miller, C.1
-
37
-
-
0023709415
-
Potassium blocks barium permeation through a calcium-activated potassium channel
-
Neyton, J., and C. Miller. 1988b. Potassium blocks barium permeation through a calcium-activated potassium channel. J. Gen. Physiol. 92:549-567. http://dx.doi.org/10.1085/jgp.92.5.549
-
(1988)
J. Gen. Physiol
, vol.92
, pp. 549-567
-
-
Neyton, J.1
Miller, C.2
-
38
-
-
33846625994
-
Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels
-
Noskov, S.Y., and B. Roux. 2007. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J. Gen. Physiol. 129:135-143. http://dx.doi.org/10.1085/jgp.200609633
-
(2007)
J. Gen. Physiol.
, vol.129
, pp. 135-143
-
-
Noskov, S.Y.1
Roux, B.2
-
39
-
-
7244251461
-
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
-
Noskov, S.Y., S. Bernèche, and B. Roux. 2004. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature. 431:830-834. http://dx.doi .org/10.1038/nature02943
-
(2004)
Nature
, vol.431
, pp. 830-834
-
-
Noskov, S.Y.1
Bernèche, S.2
Roux, B.3
-
40
-
-
2342517139
-
MCMC for hidden Markov models incorporating aggregation of states and filtering
-
Rosales, R.A. 2004. MCMC for hidden Markov models incorporating aggregation of states and filtering. Bull. Math. Biol. 66:1173-1199. http://dx.doi.org/10.1016/j.bulm.2003.12.001
-
(2004)
Bull. Math. Biol
, vol.66
, pp. 1173-1199
-
-
Rosales, R.A.1
-
41
-
-
77953576876
-
Exploring the ion selectivity properties of a large number of simplified binding site models
-
Roux, B. 2010. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophys. J. 98:2877-2885. http://dx.doi.org/10.1016/j.bpj.2010.03.038
-
(2010)
Biophys. J
, vol.98
, pp. 2877-2885
-
-
Roux, B.1
-
42
-
-
79959753998
-
MCMC estimation of Markov models for ion channels
-
Siekmann, I., L.E. Wagner II, D. Yule, C. Fox, D. Bryant, E.J. Crampin, and J. Sneyd. 2011. MCMC estimation of Markov models for ion channels. Biophys. J. 100:1919-1929. http://dx.doi .org/10.1016/j.bpj.2011.02.059
-
(2011)
Biophys. J
, vol.100
, pp. 1919-1929
-
-
Siekmann, I.1
Wagner II, L.E.2
Yule, D.3
Fox, C.4
Bryant, D.5
Crampin, E.J.6
Sneyd, J.7
-
44
-
-
44349157807
-
Molecular mechanism of pH sensing in KcsA potassium channels
-
Thompson, A.N., D.J. Posson, P.V. Parsa, and C.M. Nimigean. 2008. Molecular mechanism of pH sensing in KcsA potassium channels. Proc. Natl. Acad. Sci. USA. 105:6900-6905. http://dx.doi.org/10 .1073/pnas.0800873105
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 6900-6905
-
-
Thompson, A.N.1
Posson, D.J.2
Parsa, P.V.3
Nimigean, C.M.4
-
46
-
-
38049095537
-
+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints
-
+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints. J. Mol. Biol. 376:13-22. http://dx.doi.org/10.1016/ j.jmb.2007.11.059
-
(2008)
J. Mol. Biol
, vol.376
, pp. 13-22
-
-
Varma, S.1
Sabo, D.2
Rempe, S.B.3
-
49
-
-
77955423895
-
+ selectivity from high-resolution structures of an open K+ channel pore
-
+ channel pore. Nat. Struct. Mol. Biol. 17:1019-1023. http://dx.doi.org/10.1038/ nsmb.1865
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 1019-1023
-
-
Ye, S.1
Li, Y.2
Jiang, Y.3
-
50
-
-
0142185496
-
The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates
-
+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J. Mol. Biol. 333:965-975. http://dx.doi.org/10.1016/ j.jmb.2003.09.022
-
(2003)
J. Mol. Biol
, vol.333
, pp. 965-975
-
-
Zhou, Y.1
MacKinnon, R.2
|