-
1
-
-
0017174518
-
Distribution of lipids in cytoplasmic and outer membranes of Escherichia coli K12
-
E.J.J. Lugtenberg, and R. Peters Distribution of lipids in cytoplasmic and outer membranes of Escherichia coli K12 Biochim. Biophys. Acta 441 1976 38 47
-
(1976)
Biochim. Biophys. Acta
, vol.441
, pp. 38-47
-
-
Lugtenberg, E.J.J.1
Peters, R.2
-
2
-
-
0015513499
-
Changes in permeability of Staphylococcus aureus and derived liposomes with varying lipid composition
-
C.W. Haest, and J. de Gier L.L. van Deenen Changes in permeability of Staphylococcus aureus and derived liposomes with varying lipid composition Biochim. Biophys. Acta 255 1972 720 733
-
(1972)
Biochim. Biophys. Acta
, vol.255
, pp. 720-733
-
-
Haest, C.W.1
De Gier, J.2
Van Deenen, L.L.3
-
3
-
-
38149112637
-
Outer membrane proteins: Comparing x-ray and NMR structures by MD simulations in lipid bilayers
-
K. Cox, and P.J. Bond M.S. Sansom Outer membrane proteins: comparing x-ray and NMR structures by MD simulations in lipid bilayers Eur. Biophys. J. 37 2008 131 141
-
(2008)
Eur. Biophys. J.
, vol.37
, pp. 131-141
-
-
Cox, K.1
Bond, P.J.2
Sansom, M.S.3
-
4
-
-
0038724257
-
Membrane protein dynamics versus environment: Simulations of OmpA in a micelle and in a bilayer
-
P.J. Bond, and M.S. Sansom Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer J. Mol. Biol. 329 2003 1035 1053
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 1035-1053
-
-
Bond, P.J.1
Sansom, M.S.2
-
5
-
-
84876406310
-
Influence of lipids on protein-mediated transmembrane transport
-
E.J. Denning, and O. Beckstein Influence of lipids on protein-mediated transmembrane transport Chem. Phys. Lipids 169 2013 57 71
-
(2013)
Chem. Phys. Lipids
, vol.169
, pp. 57-71
-
-
Denning, E.J.1
Beckstein, O.2
-
6
-
-
84914164224
-
Force transduction and lipid binding in MscL: A continuum-molecular approach
-
J.M. Vanegas, and M. Arroyo Force transduction and lipid binding in MscL: a continuum-molecular approach PLoS One 9 2014 e113947
-
(2014)
PLoS One
, vol.9
, pp. e113947
-
-
Vanegas, J.M.1
Arroyo, M.2
-
7
-
-
84908240911
-
Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein
-
C.F. Weise, and F.H. Login M. Wolf-Watz Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein Biophys. J. 107 2014 1950 1961
-
(2014)
Biophys. J.
, vol.107
, pp. 1950-1961
-
-
Weise, C.F.1
Login, F.H.2
Wolf-Watz, M.3
-
8
-
-
84901981469
-
E. Coli outer membrane and interactions with OmpLA
-
E.L. Wu, and P.J. Fleming W. Im E. coli outer membrane and interactions with OmpLA Biophys. J. 106 2014 2493 2502
-
(2014)
Biophys. J.
, vol.106
, pp. 2493-2502
-
-
Wu, E.L.1
Fleming, P.J.2
Im, W.3
-
9
-
-
78650383104
-
Accelerating molecular dynamics simulation using graphics processing unit
-
H.J. Myung, and R. Sakamaki S. Lee Accelerating molecular dynamics simulation using graphics processing unit Bull. Korean Chem. Soc. 31 2010 3639 3643
-
(2010)
Bull. Korean Chem. Soc.
, vol.31
, pp. 3639-3643
-
-
Myung, H.J.1
Sakamaki, R.2
Lee, S.3
-
10
-
-
46249090563
-
Anton, a special-purpose machine for molecular dynamics simulation
-
D.E. Shaw, and M.M. Deneroff S.C. Wang ANTON, a special-purpose machine for molecular dynamics simulation Commun. ACM 51 2008 91 97
-
(2008)
Commun. ACM
, vol.51
, pp. 91-97
-
-
Shaw, D.E.1
Deneroff, M.M.2
Wang, S.C.3
-
11
-
-
74049112717
-
Millisecond-scale molecular dynamics simulations on Anton
-
Storage and Analysis, SC 2009, Portland, OR. Article No. 39. ACM, New York.
-
Shaw, D. E., R. O. Dror,..., B. Towles. 2009. Millisecond-scale molecular dynamics simulations on ANTON. In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, SC 2009, Portland, OR. Article No. 39. ACM, New York.
-
(2009)
Proceedings of the Conference on High Performance Computing Networking
-
-
Shaw, D.E.1
Dror, R.O.2
Towles, B.3
-
12
-
-
84904181910
-
Lateral opening and exit pore formation are required for BamA function
-
N. Noinaj, and A.J. Kuszak S.K. Buchanan Lateral opening and exit pore formation are required for BamA function Structure 22 2014 1055 1062
-
(2014)
Structure
, vol.22
, pp. 1055-1062
-
-
Noinaj, N.1
Kuszak, A.J.2
Buchanan, S.K.3
-
14
-
-
84909989886
-
Microsecond molecular dynamics simulations of lipid mixing
-
C. Hong, D.P. Tieleman, and Y. Wang Microsecond molecular dynamics simulations of lipid mixing Langmuir 30 2014 11993 12001
-
(2014)
Langmuir
, vol.30
, pp. 11993-12001
-
-
Hong, C.1
Tieleman, D.P.2
Wang, Y.3
-
15
-
-
0034907678
-
Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa
-
R.D. Lins, and T.P. Straatsma Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa Biophys. J. 81 2001 1037 1046
-
(2001)
Biophys. J.
, vol.81
, pp. 1037-1046
-
-
Lins, R.D.1
Straatsma, T.P.2
-
16
-
-
0001216964
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995)
-
W.D. Cornell, and P. Cieplak P.A. Coleman A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995) J. Am. Chem. Soc. 118 1996 2309
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 2309
-
-
Cornell, W.D.1
Cieplak, P.2
Coleman, P.A.3
-
17
-
-
33751155339
-
Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development
-
R.J. Woods, and R.A. Dwek B. Fraser-Reid Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development J. Phys. Chem. 99 1995 3832 3846
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 3832-3846
-
-
Woods, R.J.1
Dwek, R.A.2
Fraser-Reid, B.3
-
18
-
-
80855139866
-
Electroporation of the E. Coli and S. Aureus membranes: Molecular dynamics simulations of complex bacterial membranes
-
T.J. Piggot, D.A. Holdbrook, and S. Khalid Electroporation of the E. coli and S. aureus membranes: molecular dynamics simulations of complex bacterial membranes J. Phys. Chem. B 115 2011 13381 13388
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 13381-13388
-
-
Piggot, T.J.1
Holdbrook, D.A.2
Khalid, S.3
-
19
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
C. Oostenbrink, and A. Villa W.F. van Gunsteren A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 25 2004 1656 1676
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Van Gunsteren, W.F.3
-
20
-
-
84884303247
-
Molecular dynamics and NMR spectroscopy studies of E. Coli lipopolysaccharide structure and dynamics
-
E.L. Wu, and O. Engström W. Im Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics Biophys. J. 105 2013 1444 1455
-
(2013)
Biophys. J.
, vol.105
, pp. 1444-1455
-
-
Wu, E.L.1
Engström, O.2
Im, W.3
-
21
-
-
55349124614
-
Additive empirical force field for hexopyranose monosaccharides
-
O. Guvench, and S.N. Greene A.D. Mackerell Jr. Additive empirical force field for hexopyranose monosaccharides J. Comput. Chem. 29 2008 2543 2564
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 2543-2564
-
-
Guvench, O.1
Greene, S.N.2
Mackerell, Jr.A.D.3
-
22
-
-
73349137333
-
CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses
-
O. Guvench, and E.R. Hatcher A.D. Mackerell CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses J. Chem. Theory Comput. 5 2009 2353 2370
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2353-2370
-
-
Guvench, O.1
Hatcher, E.R.2
Mackerell, A.D.3
-
23
-
-
70349125512
-
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose
-
E. Hatcher, O. Guvench, and A.D. Mackerell CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose J. Phys. Chem. B 113 2009 12466 12476
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 12466-12476
-
-
Hatcher, E.1
Guvench, O.2
Mackerell, A.D.3
-
24
-
-
80053944070
-
CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling
-
O. Guvench, and S.S. Mallajosyula A.D. Mackerell Jr. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling J. Chem. Theory Comput. 7 2011 3162 3180
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3162-3180
-
-
Guvench, O.1
Mallajosyula, S.S.2
Mackerell, Jr.A.D.3
-
25
-
-
79960182810
-
Development of the CHARMM force field for lipids
-
R.W. Pastor, and A.D. Mackerell Jr. Development of the CHARMM force field for lipids J. Phys. Chem. Lett. 2 2011 1526 1532
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 1526-1532
-
-
Pastor, R.W.1
Mackerell, Jr.A.D.2
-
26
-
-
84857082110
-
CHARMM additive all-atom force field for phosphate and sulfate linked to carbohydrates
-
S.S. Mallajosyula, and O. Guvench A.D. Mackerell Jr. CHARMM additive all-atom force field for phosphate and sulfate linked to carbohydrates J. Chem. Theory Comput. 8 2012 759 776
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 759-776
-
-
Mallajosyula, S.S.1
Guvench, O.2
Mackerell, Jr.A.D.3
-
27
-
-
22244452943
-
Membrane electroporation: A molecular dynamics simulation
-
M. Tarek Membrane electroporation: a molecular dynamics simulation Biophys. J. 88 2005 4045 4053
-
(2005)
Biophys. J.
, vol.88
, pp. 4045-4053
-
-
Tarek, M.1
-
28
-
-
4544356700
-
The molecular basis of electroporation
-
D.P. Tieleman The molecular basis of electroporation BMC Biochem. 5 2004 10
-
(2004)
BMC Biochem.
, vol.5
, pp. 10
-
-
Tieleman, D.P.1
-
29
-
-
84892673864
-
+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM
-
+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM Proteins 82 2014 240 249
-
(2014)
Proteins
, vol.82
, pp. 240-249
-
-
Song, J.1
Ji, C.2
Zhang, J.Z.3
-
30
-
-
84856927958
-
Ion binding and internal hydration in the multidrug resistance secondary active transporter NorM investigated by molecular dynamics simulations
-
S. Vanni, and P. Campomanes U. Rothlisberger Ion binding and internal hydration in the multidrug resistance secondary active transporter NorM investigated by molecular dynamics simulations Biochemistry 51 2012 1281 1287
-
(2012)
Biochemistry
, vol.51
, pp. 1281-1287
-
-
Vanni, S.1
Campomanes, P.2
Rothlisberger, U.3
-
31
-
-
84904541300
-
The NorM MATE transporter from N. Gonorrhoeae: Insights into drug and ion binding from atomistic molecular dynamics simulations
-
Y.M. Leung, and D.A. Holdbrook S. Khalid The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations Biophys. J. 107 2014 460 468
-
(2014)
Biophys. J.
, vol.107
, pp. 460-468
-
-
Leung, Y.M.1
Holdbrook, D.A.2
Khalid, S.3
-
32
-
-
33748310520
-
Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism
-
M.A. Seeger, and A. Schiefner K.M. Pos Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism Science 313 2006 1295 1298
-
(2006)
Science
, vol.313
, pp. 1295-1298
-
-
Seeger, M.A.1
Schiefner, A.2
Pos, K.M.3
-
33
-
-
3242890387
-
Interactions underlying assembly of the Escherichia coli AcrAB-TolC multidrug efflux system
-
T. Touzé, and J. Eswaran V. Koronakis Interactions underlying assembly of the Escherichia coli AcrAB-TolC multidrug efflux system Mol. Microbiol. 53 2004 697 706
-
(2004)
Mol. Microbiol.
, vol.53
, pp. 697-706
-
-
Touzé, T.1
Eswaran, J.2
Koronakis, V.3
-
34
-
-
0034426126
-
Substrate specificities of MexAB-OprM, MexCD-OprJ, and MexXY-oprM efflux pumps in Pseudomonas aeruginosa
-
N. Masuda, and E. Sakagawa T. Nishino Substrate specificities of MexAB-OprM, MexCD-OprJ, and MexXY-oprM efflux pumps in Pseudomonas aeruginosa Antimicrob. Agents Chemother. 44 2000 3322 3327
-
(2000)
Antimicrob. Agents Chemother.
, vol.44
, pp. 3322-3327
-
-
Masuda, N.1
Sakagawa, E.2
Nishino, T.3
-
35
-
-
0032882679
-
Contribution of the MexAB-OprM multidrug efflux system to the β-lactam resistance of penicillin-binding protein and β-lactamase-derepressed mutants of Pseudomonas aeruginosa
-
R. Srikumar, E. Tsang, and K. Poole Contribution of the MexAB-OprM multidrug efflux system to the β-lactam resistance of penicillin-binding protein and β-lactamase-derepressed mutants of Pseudomonas aeruginosa J. Antimicrob. Chemother. 44 1999 537 540
-
(1999)
J. Antimicrob. Chemother.
, vol.44
, pp. 537-540
-
-
Srikumar, R.1
Tsang, E.2
Poole, K.3
-
36
-
-
84902288609
-
Efflux pump-mediated antibiotics resistance: Insights from computational structural biology
-
N. Fischer, and M. Raunest C. Kandt Efflux pump-mediated antibiotics resistance: insights from computational structural biology Interdiscip. Sci. 6 2014 1 12
-
(2014)
Interdiscip. Sci.
, vol.6
, pp. 1-12
-
-
Fischer, N.1
Raunest, M.2
Kandt, C.3
-
37
-
-
80052601598
-
Three ways in, one way out: Water dynamics in the trans-membrane domains of the inner membrane translocase AcrB
-
N. Fischer, and C. Kandt Three ways in, one way out: water dynamics in the trans-membrane domains of the inner membrane translocase AcrB Proteins 79 2011 2871 2885
-
(2011)
Proteins
, vol.79
, pp. 2871-2885
-
-
Fischer, N.1
Kandt, C.2
-
38
-
-
77955477744
-
Functional rotation of the transporter AcrB: Insights into drug extrusion from simulations
-
R. Schulz, and A.V. Vargiu P. Ruggerone Functional rotation of the transporter AcrB: insights into drug extrusion from simulations PLOS Comput. Biol. 6 2010 e1000806
-
(2010)
PLOS Comput. Biol.
, vol.6
, pp. e1000806
-
-
Schulz, R.1
Vargiu, A.V.2
Ruggerone, P.3
-
39
-
-
84870295542
-
Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment
-
D.A. Holdbrook, and T.J. Piggot S. Khalid Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment Biochim. Biophys. Acta 1828 2013 715 723
-
(2013)
Biochim. Biophys. Acta
, vol.1828
, pp. 715-723
-
-
Holdbrook, D.A.1
Piggot, T.J.2
Khalid, S.3
-
40
-
-
84870233517
-
Conformational dynamics and membrane interactions of the E. Coli outer membrane protein FecA: A molecular dynamics simulation study
-
T.J. Piggot, D.A. Holdbrook, and S. Khalid Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: a molecular dynamics simulation study Biochim. Biophys. Acta 1828 2013 284 293
-
(2013)
Biochim. Biophys. Acta
, vol.1828
, pp. 284-293
-
-
Piggot, T.J.1
Holdbrook, D.A.2
Khalid, S.3
-
41
-
-
84863012509
-
Substrate specificity within a family of outer membrane carboxylate channels
-
E. Eren, and J. Vijayaraghavan B. van den Berg Substrate specificity within a family of outer membrane carboxylate channels PLoS Biol. 10 2012 e1001242
-
(2012)
PLoS Biol.
, vol.10
, pp. e1001242
-
-
Eren, E.1
Vijayaraghavan, J.2
Van Den Berg, B.3
-
42
-
-
33644903806
-
Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa
-
S. Tamber, M.M. Ochs, and R.E. Hancock Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa J. Bacteriol. 188 2006 45 54
-
(2006)
J. Bacteriol.
, vol.188
, pp. 45-54
-
-
Tamber, S.1
Ochs, M.M.2
Hancock, R.E.3
-
43
-
-
33748456679
-
Crystal structure of osmoporin OmpC from E. Coli at 2.0 Å
-
A. Baslé, and G. Rummel T. Schirmer Crystal structure of osmoporin OmpC from E. coli at 2.0 Å J. Mol. Biol. 362 2006 933 942
-
(2006)
J. Mol. Biol.
, vol.362
, pp. 933-942
-
-
Baslé, A.1
Rummel, G.2
Schirmer, T.3
-
44
-
-
0029645574
-
The structure of OmpF porin in a tetragonal crystal form
-
S.W. Cowan, and R.M. Garavito T. Schirmer The structure of OmpF porin in a tetragonal crystal form Structure 3 1995 1041 1050
-
(1995)
Structure
, vol.3
, pp. 1041-1050
-
-
Cowan, S.W.1
Garavito, R.M.2
Schirmer, T.3
-
45
-
-
0020444488
-
Role of porin proteins OmpF and OmpC in the permeation of β-lactams
-
A. Jaffe, Y.A. Chabbert, and O. Semonin Role of porin proteins OmpF and OmpC in the permeation of β-lactams Antimicrob. Agents Chemother. 22 1982 942 948
-
(1982)
Antimicrob. Agents Chemother.
, vol.22
, pp. 942-948
-
-
Jaffe, A.1
Chabbert, Y.A.2
Semonin, O.3
-
46
-
-
65749115023
-
How β-lactam antibiotics enter bacteria: A dialogue with the porins
-
C.E. James, and K.R. Mahendran J.M. Pagès How β-lactam antibiotics enter bacteria: a dialogue with the porins PLoS One 4 2009 e5453
-
(2009)
PLoS One
, vol.4
, pp. e5453
-
-
James, C.E.1
Mahendran, K.R.2
Pagès, J.M.3
-
47
-
-
33846113922
-
An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane
-
T.F. Moraes, and M. Bains N.C. Strynadka An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane Nat. Struct. Mol. Biol. 14 2007 85 87
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 85-87
-
-
Moraes, T.F.1
Bains, M.2
Strynadka, N.C.3
-
48
-
-
76049107193
-
Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate
-
P. Pongprayoon, and O. Beckstein M.S. Sansom Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate Proc. Natl. Acad. Sci. USA 106 2009 21614 21618
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 21614-21618
-
-
Pongprayoon, P.1
Beckstein, O.2
Sansom, M.S.3
-
49
-
-
0029830142
-
The role of specific lysine residues in the passage of anions through the Pseudomonas aeruginosa porin OprP
-
A. Sukhan, and R.E.W. Hancock The role of specific lysine residues in the passage of anions through the Pseudomonas aeruginosa porin OprP J. Biol. Chem. 271 1996 21239 21242
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 21239-21242
-
-
Sukhan, A.1
Hancock, R.E.W.2
-
50
-
-
84938486901
-
Tuning the affinity of anion binding sites in porin channels with negatively charged residues: Molecular details for OprP
-
N. Modi, and I. Bárcena-Uribarri U. Kleinekathöfer Tuning the affinity of anion binding sites in porin channels with negatively charged residues: molecular details for OprP ACS Chem. Biol. 2014
-
(2014)
ACS Chem. Biol.
-
-
Modi, N.1
Bárcena-Uribarri, I.2
Kleinekathöfer, U.3
-
51
-
-
84882627597
-
Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: Effects of charge and solvation
-
N. Modi, and I. Bárcena-Uribarri U. Kleinekathöfer Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation Biochemistry 52 2013 5522 5532
-
(2013)
Biochemistry
, vol.52
, pp. 5522-5532
-
-
Modi, N.1
Bárcena-Uribarri, I.2
Kleinekathöfer, U.3
-
53
-
-
84876924253
-
Toward understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa
-
E. Eren, and J. Parkin B. van den Berg Toward understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa J. Biol. Chem. 288 2013 12042 12053
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 12042-12053
-
-
Eren, E.1
Parkin, J.2
Van Den Berg, B.3
-
54
-
-
84908301345
-
Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa
-
J. Parkin, and S. Khalid Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa Biophys. J. 107 2014 1853 1861
-
(2014)
Biophys. J.
, vol.107
, pp. 1853-1861
-
-
Parkin, J.1
Khalid, S.2
-
55
-
-
77954911184
-
Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF
-
A. Kumar, and E. Hajjar M. Ceccarelli Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF J. Phys. Chem. B 114 2010 9608 9616
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 9608-9616
-
-
Kumar, A.1
Hajjar, E.2
Ceccarelli, M.3
-
56
-
-
84859962388
-
Antibiotic permeation across the OmpF channel: Modulation of the affinity site in the presence of magnesium
-
P.R. Singh, and M. Ceccarelli K.R. Mahendran Antibiotic permeation across the OmpF channel: modulation of the affinity site in the presence of magnesium J. Phys. Chem. B 116 2012 4433 4438
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 4433-4438
-
-
Singh, P.R.1
Ceccarelli, M.2
Mahendran, K.R.3
-
57
-
-
78149432908
-
Structural and dynamical properties of the porins OmpF and OmpC: Insights from molecular simulations
-
A. Kumar, and E. Hajjar M. Ceccarelli Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations J. Phys. Condens. Matter 22 2010 454125
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 454125
-
-
Kumar, A.1
Hajjar, E.2
Ceccarelli, M.3
-
58
-
-
80855156716
-
Molecular simulation approaches to membrane proteins
-
P.J. Stansfeld, and M.S.P. Sansom Molecular simulation approaches to membrane proteins Structure 19 2011 1562 1572
-
(2011)
Structure
, vol.19
, pp. 1562-1572
-
-
Stansfeld, P.J.1
Sansom, M.S.P.2
-
59
-
-
23044476985
-
Molecular dynamics simulations of proteins in lipid bilayers
-
J. Gumbart, and Y. Wang K. Schulten Molecular dynamics simulations of proteins in lipid bilayers Curr. Opin. Struct. Biol. 15 2005 423 431
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 423-431
-
-
Gumbart, J.1
Wang, Y.2
Schulten, K.3
-
60
-
-
2942564158
-
The simulation approach to bacterial outer membrane proteins [Review]
-
P.J. Bond, and M.S.P. Sansom The simulation approach to bacterial outer membrane proteins [Review] Mol. Membr. Biol. 21 2004 151 161
-
(2004)
Mol. Membr. Biol.
, vol.21
, pp. 151-161
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
62
-
-
80052503022
-
Computational electrophysiology: The molecular dynamics of ion channel permeation and selectivity in atomistic detail
-
C. Kutzner, and H. Grubmüller U. Zachariae Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail Biophys. J. 101 2011 809 817
-
(2011)
Biophys. J.
, vol.101
, pp. 809-817
-
-
Kutzner, C.1
Grubmüller, H.2
Zachariae, U.3
-
63
-
-
70450198123
-
High-resolution architecture of the outer membrane of the Gram-negative bacteria Roseobacter denitrificans
-
S. Jarosławski, and K. Duquesne S. Scheuring High-resolution architecture of the outer membrane of the Gram-negative bacteria Roseobacter denitrificans Mol. Microbiol. 74 2009 1211 1222
-
(2009)
Mol. Microbiol.
, vol.74
, pp. 1211-1222
-
-
Jarosławski, S.1
Duquesne, K.2
Scheuring, S.3
-
64
-
-
84876890599
-
Reduced lateral mobility of lipids and proteins in crowded membranes
-
J.E. Goose, and M.S.P. Sansom Reduced lateral mobility of lipids and proteins in crowded membranes PLOS Comput. Biol. 9 2013 e1003033
-
(2013)
PLOS Comput. Biol.
, vol.9
, pp. e1003033
-
-
Goose, J.E.1
Sansom, M.S.P.2
-
65
-
-
84908093537
-
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems
-
M. Chavent, and T. Reddy M.S. Sansom Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems Faraday Discuss. 169 2014 455 475
-
(2014)
Faraday Discuss.
, vol.169
, pp. 455-475
-
-
Chavent, M.1
Reddy, T.2
Sansom, M.S.3
-
66
-
-
84934928427
-
The membranes of Gram-negative bacteria: Progress in molecular modelling and simulation
-
S. Khalid, and N.A. Berglund J. Parkin The membranes of Gram-negative bacteria: progress in molecular modelling and simulation Biochem. Soc. Trans. 43 2015 162 167
-
(2015)
Biochem. Soc. Trans.
, vol.43
, pp. 162-167
-
-
Khalid, S.1
Berglund, N.A.2
Parkin, J.3
-
67
-
-
84908606620
-
CHARMM-GUI Membrane Builder: Toward realistic biological membrane simulations
-
E.L. Wu, and X. Cheng W. Im CHARMM-GUI Membrane Builder: toward realistic biological membrane simulations J. Comput. Chem. 35 2014 1997 2004
-
(2014)
J. Comput. Chem.
, vol.35
, pp. 1997-2004
-
-
Wu, E.L.1
Cheng, X.2
Im, W.3
-
68
-
-
84893232800
-
MEMBUILDER: A web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program
-
M.M. Ghahremanpour, and S.S. Arab D. van der Spoel MEMBUILDER: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program Bioinformatics 30 2014 439 441
-
(2014)
Bioinformatics
, vol.30
, pp. 439-441
-
-
Ghahremanpour, M.M.1
Arab, S.S.2
Van Der Spoel, D.3
-
69
-
-
39449131104
-
Coarse-grained simulation: A high-throughput computational approach to membrane proteins
-
M.S. Sansom, K.A. Scott, and P.J. Bond Coarse-grained simulation: a high-throughput computational approach to membrane proteins Biochem. Soc. Trans. 36 2008 27 32
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 27-32
-
-
Sansom, M.S.1
Scott, K.A.2
Bond, P.J.3
-
70
-
-
78651268103
-
OMPdb: A database of β-barrel outer membrane proteins from Gram-negative bacteria
-
K.D. Tsirigos, P.G. Bagos, and S.J. Hamodrakas OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria Nucleic Acids Res. 39 2011 D324 D331
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D324-D331
-
-
Tsirigos, K.D.1
Bagos, P.G.2
Hamodrakas, S.J.3
-
71
-
-
78650186363
-
Lipidbook: A public repository for force-field parameters used in membrane simulations
-
J. Domański, and P.J. Stansfeld O. Beckstein Lipidbook: a public repository for force-field parameters used in membrane simulations J. Membr. Biol. 236 2010 255 258
-
(2010)
J. Membr. Biol.
, vol.236
, pp. 255-258
-
-
Domański, J.1
Stansfeld, P.J.2
Beckstein, O.3
-
72
-
-
84936845938
-
MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes
-
P.J. Stansfeld, and J.E. Goose M. Sansom MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes Structure 23 2015 1350 1361
-
(2015)
Structure
, vol.23
, pp. 1350-1361
-
-
Stansfeld, P.J.1
Goose, J.E.2
Sansom, M.3
|