-
1
-
-
79960353376
-
Tubulin-blocked state of VDAC studied by polymer and ATP partitioning
-
Gurnev, P. A., Rostovtseva, T. K., and Bezrukov, S. M. (2011) Tubulin-blocked state of VDAC studied by polymer and ATP partitioning FEBS Lett. 585, 2363-2366
-
(2011)
FEBS Lett.
, vol.585
, pp. 2363-2366
-
-
Gurnev, P.A.1
Rostovtseva, T.K.2
Bezrukov, S.M.3
-
2
-
-
0029854155
-
ATP flux is controlled by a voltage-gated channel from the mitochondrial outer membrane
-
Rostovtseva, T. and Colombini, M. (1996) ATP flux is controlled by a voltage-gated channel from the mitochondrial outer membrane J. Biol. Chem. 271, 28006-28008
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 28006-28008
-
-
Rostovtseva, T.1
Colombini, M.2
-
3
-
-
0025355620
-
Selectivity changes in site-directed mutants of the VDAC ion channel - Structural implications
-
Blachly-Dyson, E., Peng, S. Z., Colombini, M., and Forte, M. (1990) Selectivity changes in site-directed mutants of the VDAC ion channel-structural implications Science 247, 1233-1236
-
(1990)
Science
, vol.247
, pp. 1233-1236
-
-
Blachly-Dyson, E.1
Peng, S.Z.2
Colombini, M.3
Forte, M.4
-
4
-
-
0029685882
-
VDAC, a channel in the outer mitochondrial membrane
-
(Narahashi, T. Ed.) pp, Plenum Press, New York.
-
Colombini, M., Blachly-Dyson, E., and Forte, M. (1996) VDAC, a channel in the outer mitochondrial membrane, in Ion Channels (Narahashi, T., Ed.) pp 169-202, Plenum Press, New York.
-
(1996)
Ion Channels
, pp. 169-202
-
-
Colombini, M.1
Blachly-Dyson, E.2
Forte, M.3
-
5
-
-
0030947935
-
VDAC channels mediate and gate the flow of ATP: Implications for the regulation of mitochondrial function
-
Rostovtseva, T. and Colombini, M. (1997) VDAC channels mediate and gate the flow of ATP: Implications for the regulation of mitochondrial function Biophys. J. 72, 1954-1962
-
(1997)
Biophys. J.
, vol.72
, pp. 1954-1962
-
-
Rostovtseva, T.1
Colombini, M.2
-
6
-
-
0031967829
-
ATP transport through a single mitochondrial channel, VDAC, studied by current fluctuation analysis
-
Rostovtseva, T. K. and Bezrukov, S. M. (1998) ATP transport through a single mitochondrial channel, VDAC, studied by current fluctuation analysis Biophys. J. 74, 2365-2373
-
(1998)
Biophys. J.
, vol.74
, pp. 2365-2373
-
-
Rostovtseva, T.K.1
Bezrukov, S.M.2
-
7
-
-
0036219774
-
Dynamics of nucleotides in VDAC channels: Structure-specific noise generation
-
Rostovtseva, T. K., Komarov, A., Bezrukov, S. M., and Colombini, M. (2002) Dynamics of nucleotides in VDAC channels: Structure-specific noise generation Biophys. J. 82, 193-205
-
(2002)
Biophys. J.
, vol.82
, pp. 193-205
-
-
Rostovtseva, T.K.1
Komarov, A.2
Bezrukov, S.M.3
Colombini, M.4
-
8
-
-
34347375763
-
An N-terminal nucleotide-binding site in VDAC1: Involvement in regulating mitochondrial function
-
Yehezkel, G., Abu-Hamad, S., and Shoshan-Barmatz, V. (2007) An N-terminal nucleotide-binding site in VDAC1: Involvement in regulating mitochondrial function J. Cell. Physiol. 212, 551-561
-
(2007)
J. Cell. Physiol.
, vol.212
, pp. 551-561
-
-
Yehezkel, G.1
Abu-Hamad, S.2
Shoshan-Barmatz, V.3
-
9
-
-
33646847350
-
Nucleotide-binding sites in the voltage-dependent anion channel: Characterization and localization
-
Yehezkel, G., Hadad, N., Zaid, H., Sivan, S., and Shoshan-Barmatz, V. (2006) Nucleotide-binding sites in the voltage-dependent anion channel: Characterization and localization J. Biol. Chem. 281, 5938-5946
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 5938-5946
-
-
Yehezkel, G.1
Hadad, N.2
Zaid, H.3
Sivan, S.4
Shoshan-Barmatz, V.5
-
10
-
-
52449104836
-
VDAC regulation: Role of cytosolic proteins and mitochondrial lipids
-
Rostovtseva, T. K. and Bezrukov, S. M. (2008) VDAC regulation: Role of cytosolic proteins and mitochondrial lipids J. Bioenerg. Biomembr. 40, 163-170
-
(2008)
J. Bioenerg. Biomembr.
, vol.40
, pp. 163-170
-
-
Rostovtseva, T.K.1
Bezrukov, S.M.2
-
11
-
-
84859742434
-
VDAC inhibition by tubulin and its physiological implications
-
Rostovtseva, T. K. and Bezrukov, S. M. (2012) VDAC inhibition by tubulin and its physiological implications Biochim. Biophys. Acta, Biomembr. 1818, 1526-1535
-
(2012)
Biochim. Biophys. Acta, Biomembr.
, vol.1818
, pp. 1526-1535
-
-
Rostovtseva, T.K.1
Bezrukov, S.M.2
-
12
-
-
57749084634
-
Tubulin binding blocks mitochondrial voltage-dependent anion channel and regulates respiration
-
Rostovtseva, T. K., Sheldon, K. L., Hassanzadeh, E., Monge, C., Saks, V., Bezrukov, S. M., and Sackett, D. L. (2008) Tubulin binding blocks mitochondrial voltage-dependent anion channel and regulates respiration Proc. Natl. Acad. Sci. U.S.A. 105, 18746-18751
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 18746-18751
-
-
Rostovtseva, T.K.1
Sheldon, K.L.2
Hassanzadeh, E.3
Monge, C.4
Saks, V.5
Bezrukov, S.M.6
Sackett, D.L.7
-
13
-
-
54949088596
-
Regulation of respiration in brain mitochondria and synaptosomes: Restrictions of ADP diffusion in situ, roles of tubulin, and mitochondrial creatine kinase
-
Monge, C., Beraud, N., Kuznetsov, A. V., Rostovtseva, T., Sackett, D., Schlattner, U., Vendelin, M., and Saks, V. A. (2008) Regulation of respiration in brain mitochondria and synaptosomes: Restrictions of ADP diffusion in situ, roles of tubulin, and mitochondrial creatine kinase Mol. Cell. Biochem. 318, 94-1562
-
(2008)
Mol. Cell. Biochem.
, vol.318
, pp. 94-1562
-
-
Monge, C.1
Beraud, N.2
Kuznetsov, A.V.3
Rostovtseva, T.4
Sackett, D.5
Schlattner, U.6
Vendelin, M.7
Saks, V.A.8
-
14
-
-
78650332649
-
Free tubulin modulates mitochondrial membrane potential in cancer cells
-
Maldonado, E. N., Patnaik, J., Mullins, M. R., and Lemasters, J. J. (2011) Free tubulin modulates mitochondrial membrane potential in cancer cells Cancer Res. 70, 10192-10201
-
(2011)
Cancer Res.
, vol.70
, pp. 10192-10201
-
-
Maldonado, E.N.1
Patnaik, J.2
Mullins, M.R.3
Lemasters, J.J.4
-
15
-
-
84876936843
-
Voltage-dependent anion channels modulate mitochondrial metabolism in cancer cells regulation by tubulin and erastin
-
Maldonado, E. N., Sheldon, K. L., DeHart, D. N., Patnaik, J., Manevich, Y., Townsend, D. M., Bezrukov, S. M., Rostovtseva, T. K., and Lemasters, J. J. (2013) Voltage-dependent anion channels modulate mitochondrial metabolism in cancer cells regulation by tubulin and erastin J. Biol. Chem. 288, 11920-11929
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 11920-11929
-
-
Maldonado, E.N.1
Sheldon, K.L.2
Dehart, D.N.3
Patnaik, J.4
Manevich, Y.5
Townsend, D.M.6
Bezrukov, S.M.7
Rostovtseva, T.K.8
Lemasters, J.J.9
-
16
-
-
80054052133
-
Phosphorylation of voltage-dependent anion channel by serine/threonine kinases governs its interaction with tubulin
-
Sheldon, K. L., Maldonado, E. N., Lemasters, J. J., Rostovtseva, T. K., and Bezrukov, S. M. (2011) Phosphorylation of voltage-dependent anion channel by serine/threonine kinases governs its interaction with tubulin PloS One 6, e25539-1-e25539-10
-
(2011)
PloS One
, vol.6
-
-
Sheldon, K.L.1
Maldonado, E.N.2
Lemasters, J.J.3
Rostovtseva, T.K.4
Bezrukov, S.M.5
-
17
-
-
84896507778
-
VDAC1 topology in the outer mitochondrial membrane: The final answer
-
Guarino, F., Tomasello, M. F., Magri, A., Impellizzeri, A., Reina, S., Messina, A., and De Pinto, V. (2013) VDAC1 topology in the outer mitochondrial membrane: The final answer Biophys. J. 104, 539A-540A
-
(2013)
Biophys. J.
, vol.104
-
-
Guarino, F.1
Tomasello, M.F.2
Magri, A.3
Impellizzeri, A.4
Reina, S.5
Messina, A.6
De Pinto, V.7
-
18
-
-
0034710171
-
Cloning and recombinant expression of the la RNA-binding protein from Trypanosoma brucei
-
Westermann, S. and Weber, K. (2000) Cloning and recombinant expression of the La RNA-binding protein from Trypanosoma brucei Biochim. Biophys. Acta, Gene Struct. Expression 1492, 483-487
-
(2000)
Biochim. Biophys. Acta, Gene Struct. Expression
, vol.1492
, pp. 483-487
-
-
Westermann, S.1
Weber, K.2
-
19
-
-
56649099192
-
The crystal structure of mouse VDAC1 at 2.3 angstrom resolution reveals mechanistic insights into metabolite gating
-
Ujwal, R., Cascio, D., Colletier, J. P., Faham, S., Zhang, J., Toro, L., Ping, P. P., and Abramson, J. (2008) The crystal structure of mouse VDAC1 at 2.3 angstrom resolution reveals mechanistic insights into metabolite gating Proc. Natl. Acad. Sci. U.S.A. 105, 17742-17747
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 17742-17747
-
-
Ujwal, R.1
Cascio, D.2
Colletier, J.P.3
Faham, S.4
Zhang, J.5
Toro, L.6
Ping, P.P.7
Abramson, J.8
-
20
-
-
3843053396
-
The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography
-
Nettles, J. H., Li, H. L., Cornett, B., Krahn, J. M., Snyder, J. P., and Downing, K. H. (2004) The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography Science 305, 866-869
-
(2004)
Science
, vol.305
, pp. 866-869
-
-
Nettles, J.H.1
Li, H.L.2
Cornett, B.3
Krahn, J.M.4
Snyder, J.P.5
Downing, K.H.6
-
21
-
-
80052597892
-
Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface
-
Freedman, H., Luchko, T., Luduena, R. F., and Tuszynski, J. A. (2011) Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface Proteins 79, 2968-2982
-
(2011)
Proteins
, vol.79
, pp. 2968-2982
-
-
Freedman, H.1
Luchko, T.2
Luduena, R.F.3
Tuszynski, J.A.4
-
22
-
-
41149134824
-
Automated builder and database of protein/membrane complexes for molecular dynamics simulations
-
Jo, S., Kim, T., and Im, W. (2007) Automated builder and database of protein/membrane complexes for molecular dynamics simulations PLoS One 2, e880-1-e880-9
-
(2007)
PLoS One
, vol.2
-
-
Jo, S.1
Kim, T.2
Im, W.3
-
23
-
-
84860510775
-
Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores
-
(Gracheva, M. E. Ed.) pp; Humana Press, New York.
-
Wells, D. B., Bhattacharya, S., Carr, R., Maffeo, C., Ho, A., Comer, J., and Aksimentiev, A. (2012) Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores, in Nanopore-Based Technology (Gracheva, M. E., Ed.) pp 165-186; Humana Press, New York.
-
(2012)
Nanopore-Based Technology
, pp. 165-186
-
-
Wells, D.B.1
Bhattacharya, S.2
Carr, R.3
Maffeo, C.4
Ho, A.5
Comer, J.6
Aksimentiev, A.7
-
24
-
-
84986534166
-
New spherical-cutoff methods for long-range forces in macromolecular simulation
-
Steinbach, P. J. and Brooks, B. R. (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation J. Comput. Chem. 15, 667-683
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
25
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method J. Chem. Phys. 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
26
-
-
80052028893
-
Algorithms for constrained molecular-dynamics
-
Barth, E., Kuczera, K., Leimkuhler, B., and Skeel, R. D. (1995) Algorithms for constrained molecular-dynamics J. Comput. Chem. 16, 1192-1209
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1192-1209
-
-
Barth, E.1
Kuczera, K.2
Leimkuhler, B.3
Skeel, R.D.4
-
27
-
-
79953232070
-
Rectification of the current in alpha-hemolysin pore depends on the cation type: The alkali series probed by molecular dynamics simulations and experiments
-
Bhattacharya, S., Muzard, J., Payet, L., Mathe, J., Bockelmann, U., Aksimentiev, A., and Viasnoff, V. (2011) Rectification of the current in alpha-hemolysin pore depends on the cation type: The alkali series probed by molecular dynamics simulations and experiments J. Phys. Chem. C 115, 4255-4264
-
(2011)
J. Phys. Chem. C
, vol.115
, pp. 4255-4264
-
-
Bhattacharya, S.1
Muzard, J.2
Payet, L.3
Mathe, J.4
Bockelmann, U.5
Aksimentiev, A.6
Viasnoff, V.7
-
28
-
-
65349156366
-
Ionic current rectification through silica nanopores
-
Cruz-Chu, E. R., Aksimentiev, A., and Schulten, K. (2009) Ionic current rectification through silica nanopores J. Phys. Chem. C 113, 1850-1862
-
(2009)
J. Phys. Chem. C
, vol.113
, pp. 1850-1862
-
-
Cruz-Chu, E.R.1
Aksimentiev, A.2
Schulten, K.3
-
29
-
-
84870927064
-
Modeling and simulation of ion channels
-
Maffeo, C., Bhattacharya, S., Yoo, J., Wells, D., and Aksimentiev, A. (2012) Modeling and simulation of ion channels Chem. Rev. 112, 6250-6284
-
(2012)
Chem. Rev.
, vol.112
, pp. 6250-6284
-
-
Maffeo, C.1
Bhattacharya, S.2
Yoo, J.3
Wells, D.4
Aksimentiev, A.5
-
30
-
-
77953677764
-
Deciphering ionic current signatures of DNA transport through a nanopore
-
Aksimentiev, A. (2010) Deciphering ionic current signatures of DNA transport through a nanopore Nanoscale 2, 468-483
-
(2010)
Nanoscale
, vol.2
, pp. 468-483
-
-
Aksimentiev, A.1
-
31
-
-
77950544751
-
Principles of conduction and hydrophobic gating in K+ channels
-
Jensen, M. O., Borhani, D. W., Lindorff-Larsen, K., Maragakis, P., Jogini, V., Eastwood, M. P., Dror, R. O., and Shaw, D. E. (2010) Principles of conduction and hydrophobic gating in K+ channels Proc. Natl. Acad. Sci. U.S.A. 107, 5833-5838
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 5833-5838
-
-
Jensen, M.O.1
Borhani, D.W.2
Lindorff-Larsen, K.3
Maragakis, P.4
Jogini, V.5
Eastwood, M.P.6
Dror, R.O.7
Shaw, D.E.8
-
32
-
-
84878572294
-
Atomic-level simulation of current-voltage relationships in single-file ion channels
-
Jensen, M. O., Jogini, V., Eastwood, M. P., and Shaw, D. E. (2013) Atomic-level simulation of current-voltage relationships in single-file ion channels J. Gen. Physiol. 141, 619-632
-
(2013)
J. Gen. Physiol.
, vol.141
, pp. 619-632
-
-
Jensen, M.O.1
Jogini, V.2
Eastwood, M.P.3
Shaw, D.E.4
-
33
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD J. Comput. Biol. 26, 1781-1802
-
(2005)
J. Comput. Biol.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
34
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M., and Karplus, M. (2009) CHARMM: The biomolecular simulation program J. Comput. Chem. 30, 1545-1614
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
35
-
-
77953377650
-
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
-
Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D., and Pastor, R. W. (2010) Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types J. Phys. Chem. B 114, 7830-7843
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Freites, J.A.3
O'Connor, J.W.4
Tobias, D.J.5
Mondragon-Ramirez, C.6
Vorobyov, I.7
Mackerell, A.D.8
Pastor, R.W.9
-
36
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
37
-
-
79961012919
-
Benchmarking and analysis of protein docking performance in Rosetta v3.2
-
Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., and Gray, J. J. (2011) Benchmarking and analysis of protein docking performance in Rosetta v3.2 PLoS One 6, e22477-1-e22477-13
-
(2011)
PLoS One
, vol.6
-
-
Chaudhury, S.1
Berrondo, M.2
Weitzner, B.D.3
Muthu, P.4
Bergman, H.5
Gray, J.J.6
-
38
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang, C., Bradley, P., and Baker, D. (2007) Protein-protein docking with backbone flexibility J. Mol. Biol. 373, 503-519
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
39
-
-
40049090139
-
Scalable molecular dynamics with NAMD on the IBM blue gene/L system
-
Kumar, S., Huang, C., Zheng, G., Bohm, E., Bhatele, A., Phillips, J. C., Yu, H., and Kale, L. V. (2008) Scalable molecular dynamics with NAMD on the IBM blue gene/L system IBM J. Res. Dev. 52, 177-188
-
(2008)
IBM J. Res. Dev.
, vol.52
, pp. 177-188
-
-
Kumar, S.1
Huang, C.2
Zheng, G.3
Bohm, E.4
Bhatele, A.5
Phillips, J.C.6
Yu, H.7
Kale, L.V.8
-
40
-
-
84890794190
-
Frontiers in free energy calculations of biological systems
-
[Online early access] DOI: 10.1002/wcms.1157. Published Online: June 6, 2013.
-
Chipot, C. (2013) Frontiers in free energy calculations of biological systems. WIREs Comput. Mol. Sci. [Online early access] DOI: 10.1002/wcms.1157. Published Online: June 6, 2013.
-
(2013)
WIREs Comput. Mol. Sci.
-
-
Chipot, C.1
-
41
-
-
0027794972
-
Targeted molecular-dynamics simulation of conformational change - Application to the Tâ†R transition in insulin
-
Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. (1993) Targeted molecular-dynamics simulation of conformational change-application to the Tâ†R transition in insulin Mol. Simul. 10, 291-296
-
(1993)
Mol. Simul.
, vol.10
, pp. 291-296
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
Jacoby, E.4
Wollmer, A.5
-
42
-
-
84887289890
-
The molecular mechanism of ion-dependent gating in secondary transporters
-
Zhao, C. F. and Noskov, S. Y. (2013) The molecular mechanism of ion-dependent gating in secondary transporters PLoS Comp. Biol. 9, e1003296-1-e1003296-12
-
(2013)
PLoS Comp. Biol.
, vol.9
-
-
Zhao, C.F.1
Noskov, S.Y.2
-
43
-
-
0029633155
-
The calculation of the potential of mean force using computer-simulations
-
Roux, B. (1995) The calculation of the potential of mean force using computer-simulations Comput. Phys. Commun. 91, 275-282
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
44
-
-
0347089020
-
Energetics of ion conduction through the gramicidin channel
-
Allen, T. W., Andersen, O. S., and Roux, B. (2004) Energetics of ion conduction through the gramicidin channel Proc. Natl. Acad. Sci. U.S.A. 101, 117-122
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 117-122
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
45
-
-
81055126297
-
On the selective ion binding hypothesis for potassium channels
-
Kim, I. and Allen, T. W. (2011) On the selective ion binding hypothesis for potassium channels Proc. Natl. Acad. Sci. U.S.A. 108, 17963-17968
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 17963-17968
-
-
Kim, I.1
Allen, T.W.2
-
46
-
-
84857080087
-
The role of atomic polarization in the thermodynamics of chloroform partitioning to lipid bilayers
-
Vorobyov, I., Bennett, W. F. D., Tieleman, D. P., Allen, T. W., and Noskov, S. (2012) The role of atomic polarization in the thermodynamics of chloroform partitioning to lipid bilayers J. Chem. Theory Comput. 8, 618-628
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 618-628
-
-
Vorobyov, I.1
Bennett, W.F.D.2
Tieleman, D.P.3
Allen, T.W.4
Noskov, S.5
-
47
-
-
80054686096
-
The structural pathway for water permeation through sodium-glucose cotransporters
-
Sasseville, L., Cuervo, J. E., Lapointe, J. Y., and Noskov, S. Y. (2011) The structural pathway for water permeation through sodium-glucose cotransporters Biophys. J. 101, 1887-1895
-
(2011)
Biophys. J.
, vol.101
, pp. 1887-1895
-
-
Sasseville, L.1
Cuervo, J.E.2
Lapointe, J.Y.3
Noskov, S.Y.4
-
48
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina, M., Beglov, D., and Roux, B. (1997) Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations J. Phys. Chem. B 101, 5239-5248
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
49
-
-
48449099381
-
PBEQ-Solver for online visualization of electrostatic potential of biomolecules
-
Jo, S., Vargyas, M., Vasko-Szedlar, J., Roux, B., and Im, W. (2008) PBEQ-Solver for online visualization of electrostatic potential of biomolecules Nucleic Acids Res. 36, W270-W275
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Jo, S.1
Vargyas, M.2
Vasko-Szedlar, J.3
Roux, B.4
Im, W.5
-
50
-
-
23844459909
-
Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement
-
Chanda, B., Asamoah, O. K., Blunck, R., Roux, B., and Bezanilla, F. (2005) Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement Nature 436, 852-856
-
(2005)
Nature
, vol.436
, pp. 852-856
-
-
Chanda, B.1
Asamoah, O.K.2
Blunck, R.3
Roux, B.4
Bezanilla, F.5
-
51
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson, J. M. J., Henchman, R. H., and McCammon, J. A. (2004) Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy Biophys. J. 86, 67-74
-
(2004)
Biophys. J.
, vol.86
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
52
-
-
0041806661
-
A microscopic view of ion conduction through the K+ channel
-
Berneche, S. and Roux, B. (2003) A microscopic view of ion conduction through the K+ channel Proc. Natl. Acad. Sci. U.S.A. 100, 8644-8648
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 8644-8648
-
-
Berneche, S.1
Roux, B.2
-
53
-
-
84882330872
-
Efficient determination of protein-protein standard binding free energies from first principles
-
Gumbart, J. C., Roux, B., and Chipot, C. (2013) Efficient determination of protein-protein standard binding free energies from first principles J. Chem. Theory Comput. 9, 3789-3798
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3789-3798
-
-
Gumbart, J.C.1
Roux, B.2
Chipot, C.3
-
54
-
-
77953307336
-
Evaluations of the absolute and relative free energies for antidepressant binding to the amino acid membrane transporter LeuT with free energy simulations
-
Zhao, C. F., Caplan, D. A., and Noskov, S. Y. (2010) Evaluations of the absolute and relative free energies for antidepressant binding to the amino acid membrane transporter LeuT with free energy simulations J. Chem. Theory Comput. 6, 1900-1914
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1900-1914
-
-
Zhao, C.F.1
Caplan, D.A.2
Noskov, S.Y.3
-
55
-
-
84856747852
-
Binding modes of mu-conotoxin to the bacterial sodium channel (Na(v)Ab)
-
Chen, R. and Chung, S. H. (2012) Binding modes of mu-conotoxin to the bacterial sodium channel (Na(v)Ab) Biophys. J. 102, 483-488
-
(2012)
Biophys. J.
, vol.102
, pp. 483-488
-
-
Chen, R.1
Chung, S.H.2
-
56
-
-
77949332587
-
The electrostatics of VDAC: Implications for selectivity and gating
-
Choudhary, O. P., Ujwal, R., Kowallis, W., Coalson, R., Abramson, J., and Grabe, M. (2010) The electrostatics of VDAC: Implications for selectivity and gating J. Mol. Biol. 396, 580-592
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 580-592
-
-
Choudhary, O.P.1
Ujwal, R.2
Kowallis, W.3
Coalson, R.4
Abramson, J.5
Grabe, M.6
-
57
-
-
0034319631
-
Particle number fluctuations in a membrane channel
-
Bezrukov, S. M., Berezhkovski, A. M., Pustovoit, M. A., and Szabo, A. (2000) Particle number fluctuations in a membrane channel J. Chem. Phys. 113, 8206-8211
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 8206-8211
-
-
Bezrukov, S.M.1
Berezhkovski, A.M.2
Pustovoit, M.A.3
Szabo, A.4
-
58
-
-
0037042609
-
Channel-facilitated membrane transport: Transit probability and interactions with the channel
-
Berezhkovskii, A. M., Pustovoit, M. A., and Bezrukov, S. M. (2002) Channel-facilitated membrane transport: Transit probability and interactions with the channel J. Chem. Phys. 116, 9952-9956
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 9952-9956
-
-
Berezhkovskii, A.M.1
Pustovoit, M.A.2
Bezrukov, S.M.3
-
59
-
-
21244505884
-
Optimizing transport of metabolites through large channels: Molecule sieves with and without binding
-
Berezhkovskii, A. M. and Bezrukov, S. M. (2004) Optimizing transport of metabolites through large channels: Molecule sieves with and without binding Biophys. J. 88, L17-L19
-
(2004)
Biophys. J.
, vol.88
-
-
Berezhkovskii, A.M.1
Bezrukov, S.M.2
-
60
-
-
84865472739
-
Membrane lipid composition regulates tubulin interaction with mitochondrial voltage-dependent anion channel
-
Rostovtseva, T. K., Gurnev, P. A., Chen, M. Y., and Bezrukov, S. M. (2012) Membrane lipid composition regulates tubulin interaction with mitochondrial voltage-dependent anion channel J. Biol. Chem. 287, 29589-29598
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 29589-29598
-
-
Rostovtseva, T.K.1
Gurnev, P.A.2
Chen, M.Y.3
Bezrukov, S.M.4
-
61
-
-
79960930163
-
Modeling disordered regions in proteins using Rosetta
-
Wang, R. Y.-R., Han, Y., Krassovsky, K., Sheffler, W., Tyka, M., and Baker, D. (2011) Modeling disordered regions in proteins using Rosetta PLoS One 6, e22060-1-e22060-9
-
(2011)
PLoS One
, vol.6
-
-
Wang, R.Y.-R.1
Han, Y.2
Krassovsky, K.3
Sheffler, W.4
Tyka, M.5
Baker, D.6
-
62
-
-
22244445788
-
Imaging the permeability of alpha-hemolysin with molecular dynamics
-
Aksimentiev, A. and Schulten, K. (2005) Imaging the permeability of alpha-hemolysin with molecular dynamics Biophys. J. 88, 3745-3761
-
(2005)
Biophys. J.
, vol.88
, pp. 3745-3761
-
-
Aksimentiev, A.1
Schulten, K.2
-
63
-
-
0036389892
-
Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics, brownian dynamics, and continuum electrodiffusion theory
-
Im, W. and Roux, B. (2002) Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics, brownian dynamics, and continuum electrodiffusion theory J. Mol. Biol. 322, 851-869
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 851-869
-
-
Im, W.1
Roux, B.2
-
64
-
-
79551677025
-
Molecular dynamics studies of ion permeation in VDAC
-
Rui, H. A., Lee, K. I., Pastor, R. W., and Im, W. (2011) Molecular dynamics studies of ion permeation in VDAC Biophys. J. 100, 602-610
-
(2011)
Biophys. J.
, vol.100
, pp. 602-610
-
-
Rui, H.A.1
Lee, K.I.2
Pastor, R.W.3
Im, W.4
-
65
-
-
84865760948
-
β-Barrel mobility underlies closure of the voltage-dependent anion channel
-
Zachariae, U., Schneider, R., Briones, R., Gattin, Z., Demers, J. P., Giller, K., Maier, E., Zweckstetter, M., Griesinger, C., Becker, S., Benz, R., de Groot, B. L., and Lange, A. (2012) β-Barrel mobility underlies closure of the voltage-dependent anion channel Structure 20, 1540-1549
-
(2012)
Structure
, vol.20
, pp. 1540-1549
-
-
Zachariae, U.1
Schneider, R.2
Briones, R.3
Gattin, Z.4
Demers, J.P.5
Giller, K.6
Maier, E.7
Zweckstetter, M.8
Griesinger, C.9
Becker, S.10
Benz, R.11
De Groot, B.L.12
Lange, A.13
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