-
5
-
-
48449084244
-
-
10.1007/s11120-008-9293-2
-
T. Simonson 2008 Photosynth. Res. 97 21 10.1007/s11120-008-9293-2
-
(2008)
Photosynth. Res.
, vol.97
, pp. 21
-
-
Simonson, T.1
-
7
-
-
0030945495
-
-
10.1016/S0006-3495(97)78851-9 1997BpJ.72.2075A
-
E.G. Alexov M.R. Gunner 1997 Biophys. J. 72 2075 10.1016/S0006-3495(97) 78851-9 1997BpJ.72.2075A
-
(1997)
Biophys. J.
, vol.72
, pp. 2075
-
-
Alexov, E.G.1
Gunner, M.R.2
-
10
-
-
4644264472
-
a calculations through flexibility based sampling of a water-dominated interaction scheme
-
DOI 10.1110/ps.04785604
-
J. Warwicker 2004 Protein Sci. 13 2793 10.1110/ps.04785604 (Pubitemid 39274646)
-
(2004)
Protein Science
, vol.13
, Issue.10
, pp. 2793-2805
-
-
Warwicker, J.1
-
11
-
-
0028859420
-
-
10.1016/S0006-3495(95)80042-1 1995BpJ.69.1721Y
-
T.J. You D. Bashford 1995 Biophys. J. 69 1721 10.1016/S0006-3495(95) 80042-1 1995BpJ.69.1721Y
-
(1995)
Biophys. J.
, vol.69
, pp. 1721
-
-
You, T.J.1
Bashford, D.2
-
15
-
-
0031670370
-
Improving the accuracy of protein pK(a) calculations: Conformational averaging versus the average structure
-
DOI 10.1002/(SICI)1097-0134(19981101)33:2<145::AID-PROT1>3.0.CO;2-I
-
H.W. van Vlijmen M. Schaefer M. Karplus 1998 Proteins 33 145 10.1002/(SICI)1097-0134(19981101)33:2<145::AID-PROT1>3.0.CO;2-I (Pubitemid 28457969)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.33
, Issue.2
, pp. 145-158
-
-
Van Vlijmen, H.W.T.1
Schaefer, M.2
Karplus, M.3
-
18
-
-
33645675121
-
-
10.1021/jp054814j
-
J. Makowska K. Bagiñska M. Makowski A. Jagielska A. Liwo F. Kasprzykowski L. Chmurzyñski H.A. Scheraga 2006 J. Phys. Chem. B 110 4451 10.1021/jp054814j
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 4451
-
-
Makowska, J.1
Bagiñska, K.2
Makowski, M.3
Jagielska, A.4
Liwo, A.5
Kasprzykowski, F.6
Chmurzyñski, L.7
Scheraga, H.A.8
-
21
-
-
0037305552
-
On the evaluation and optimization of protein X-ray structures for pKa calculations
-
DOI 10.1110/ps.0229903
-
J.E. Nielsen J.A. McCammon 2003 Protein Sci. 12 313 10.1110/ps.0229903 (Pubitemid 36120344)
-
(2003)
Protein Science
, vol.12
, Issue.2
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
25
-
-
33644745556
-
Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine
-
DOI 10.1021/jp056456q
-
M. Machuqueiro A.M. Baptista 2006 J. Phys. Chem. B 110 2927 10.1021/jp056456q (Pubitemid 43342889)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.6
, pp. 2927-2933
-
-
Machuqueiro, M.1
Baptista, A.M.2
-
27
-
-
0032769471
-
A fast and simple method to calculate protonation states in proteins
-
DOI 10.1002/(SICI)1097-0134(19990901)36:4<474::AID-PROT12>3.0.CO;2- V
-
L. Sandberg O. Edholm 1999 Proteins: Struct. Funct. Genet. 36 474 10.1002/(SICI)1097-0134(19990901)36:4<474::AID-PROT12>3.0.CO;2-V (Pubitemid 29387747)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.36
, Issue.4
, pp. 474-483
-
-
Sandberg, L.1
Edholm, O.2
-
29
-
-
0037104738
-
a from dielectric continuum theory
-
DOI 10.1021/jp020847c
-
D.M. Chipman 2002 J. Phys. Chem. A 106 7413 10.1021/jp020847c (Pubitemid 35382586)
-
(2002)
Journal of Physical Chemistry A
, vol.106
, Issue.32
, pp. 7413-7422
-
-
Chipman, D.M.1
-
34
-
-
33749189483
-
Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations
-
DOI 10.1016/j.bbabio.2006.06.005, PII S0005272806001861
-
M.R. Gunner J. Mao Y. Song J. Kim 2006 Biochim. Biophys. Acta 1757 942 10.1016/j.bbabio.2006.06.005 (Pubitemid 44472483)
-
(2006)
Biochimica et Biophysica Acta - Bioenergetics
, vol.1757
, Issue.8
, pp. 942-968
-
-
Gunner, M.R.1
Mao, J.2
Song, Y.3
Kim, J.4
-
35
-
-
1542320003
-
Structural Interpretation of pH and Salt-Dependent Processes in Proteins with Computational Methods
-
DOI 10.1016/S0076-6879(04)80002-8
-
B. García-Moreno C.A. Fitch 2004 Meth. Enzymol. 380 20 10.1016/S0076-6879(04)80002-8 (Pubitemid 38297489)
-
(2004)
Methods in Enzymology
, vol.380
, pp. 20-51
-
-
Garcia-Moreno E, B.1
Fitch, C.A.2
-
37
-
-
68249126139
-
-
10.1016/j.tibs.2009.05.001
-
M. Colombini 2009 Trends Biochem. Sci. 34 382 10.1016/j.tibs.2009.05.001
-
(2009)
Trends Biochem. Sci.
, vol.34
, pp. 382
-
-
Colombini, M.1
-
40
-
-
0036105803
-
Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins
-
DOI 10.1110/ps.4910102
-
U. Zachariae A. Koumanov H. Engelhardt A. Karshikoff 2002 Protein Sci. 11 1309 10.1110/ps.4910102 (Pubitemid 34547203)
-
(2002)
Protein Science
, vol.11
, Issue.6
, pp. 1309-1319
-
-
Zachariae, U.1
Koumanov, A.2
Engelhardt, H.3
Karshikoff, A.4
-
43
-
-
1142298543
-
-
10.1016/S0006-3495(04)74148-X 2004BpJ.86.690V
-
S. Varma E. Jakobsson 2004 Biophys. J. 86 690 10.1016/S0006-3495(04) 74148-X 2004BpJ.86.690V
-
(2004)
Biophys. J.
, vol.86
, pp. 690
-
-
Varma, S.1
Jakobsson, E.2
-
45
-
-
0030447720
-
Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore
-
DOI 10.1126/science.274.5294.1859
-
L. Song M.R. Hobaugh C. Shustak S. Cheley H. Bayley J.E. Gouaux 1996 Science 274 1859 10.1126/science.274.5294.1859 1996Sci.274.1859S (Pubitemid 26424757)
-
(1996)
Science
, vol.274
, Issue.5294
, pp. 1859-1866
-
-
Song, L.1
Hobaugh, M.R.2
Shustak, C.3
Cheley, S.4
Bayley, H.5
Gouaux, J.E.6
-
46
-
-
0242301631
-
Electrostatic Influence on Ion Transport through the αHL Channel
-
DOI 10.1007/s00232-003-0615-1
-
M. Misakian J.J. Kasianowicz 2003 J. Membrane Biol. 195 137 10.1007/s00232-003-0615-1 (Pubitemid 37338956)
-
(2003)
Journal of Membrane Biology
, vol.195
, Issue.3
, pp. 137-146
-
-
Misakian, M.1
Kasianowicz, J.J.2
-
47
-
-
15244338641
-
Ion permeation through the α-hemolysin channel: Theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory
-
DOI 10.1529/biophysj.104.044008
-
S.Y. Noskov W. Im B. Roux 2004 Biophys. J. 87 2299 10.1529/biophysj.104. 044008 2004BpJ.87.2299N (Pubitemid 41071331)
-
(2004)
Biophysical Journal
, vol.87
, Issue.4
, pp. 2299-2309
-
-
Noskov, S.Yu.1
Im, W.2
Roux, B.3
-
48
-
-
12344270062
-
Hybrid MD-Nernst Planck model of α-hemolysin conductance properties
-
DOI 10.1080/08927020412331308467
-
I. Cozmuta J.T. O'Keeffe D. Bose V. Stolc 2005 Molec. Simul. 31 79 10.1080/08927020412331308467 (Pubitemid 40121098)
-
(2005)
Molecular Simulation
, vol.31
, Issue.2-3
, pp. 79-93
-
-
Cozmuta, I.1
O'Keeffe, J.T.2
Bose, D.3
Stolc, V.4
-
49
-
-
22244445788
-
Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
-
DOI 10.1529/biophysj.104.058727
-
A. Aksimentiev K. Schulten 2005 Biophys. J. 88 3745 10.1529/biophysj.104. 058727 (Pubitemid 40991090)
-
(2005)
Biophysical Journal
, vol.88
, Issue.6
, pp. 3745-3761
-
-
Aksimentiev, A.1
Schulten, K.2
-
50
-
-
34848830419
-
Exploring transmembrane transport through α -hemolysin with grid-steered molecular dynamics
-
DOI 10.1063/1.2770738
-
D.B. Wells V. Abramkina A. Aksimentiev 2007 J. Chem. Phys. 127 125101 10.1063/1.2770738 2007JChPh.127l5101W (Pubitemid 47505206)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.12
, pp. 125101
-
-
Wells, D.B.1
Abramkina, V.2
Aksimentiev, A.3
-
55
-
-
0034214419
-
Electrostatic properties of bovine β-Lactoglobulin
-
DOI 10.1002/(SICI)1097-0134(20000601)39:4<317::AID-PROT50>3.0.CO;2- W
-
F. Fogolari L. Ragona S. Licciardi S. Romagnoli R. Michelutti R. Ugolini H. Molinari 2000 Proteins: Struct. Funct. Genet. 39 317 10.1002/(SICI)1097- 0134(20000601)39:4<317::AID-PROT50>3.0.CO;2-W (Pubitemid 30414170)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.39
, Issue.4
, pp. 317-330
-
-
Fogolari, F.1
Ragona, L.2
Licciardi, S.3
Romagnoli, S.4
Michelutti, R.5
Ugolini, R.6
Molinari, H.7
-
57
-
-
0029633152
-
-
10.1016/0010-4655(95)00043-F 1995CoPhC.91.57M
-
J.D. Madura J.M. Briggs R.C. Wade M.E. Davis B.A. Luty A. Ilin J. Antosiewicz M.K. Gilson B. Bagheri L.R. Scott J.A. McCammon 1995 Comput. Phys. Commun. 91 57 10.1016/0010-4655(95)00043-F 1995CoPhC.91.57M
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 57
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davis, M.E.4
Luty, B.A.5
Ilin, A.6
Antosiewicz, J.7
Gilson, M.K.8
Bagheri, B.9
Scott, L.R.10
McCammon, J.A.11
-
58
-
-
84870649266
-
-
The protein data bank, http://www.rcsb.org/pdb explore/explore.do? structureId=7AHL
-
The Protein Data Bank
-
-
-
61
-
-
0028980231
-
-
10.1016/S0006-3495(95)79879-4 1995BpJ.69.94K
-
J.J. Kasianowicz S.M. Bezrukov 1995 Biophys. J. 69 94 10.1016/S0006-3495(95)79879-4 1995BpJ.69.94K
-
(1995)
Biophys. J.
, vol.69
, pp. 94
-
-
Kasianowicz, J.J.1
Bezrukov, S.M.2
|