-
1
-
-
55249113656
-
The use of detergents to purify membrane proteins
-
Chapter 4, Units
-
Arnold, T.; Linke, D. The use of detergents to purify membrane proteins. Current Protocols in Protein Science; 2008; Chapter 4, Units 53:4.8.1-4.8.30.
-
(2008)
Current Protocols in Protein Science
, pp. 53481-54830
-
-
Arnold, T.1
Linke, D.2
-
2
-
-
33947172767
-
Detergents for the stabilization and crystallization of membrane proteins
-
Privé, G. Detergents for the stabilization and crystallization of membrane proteins Methods 2007, 41, 388-397
-
(2007)
Methods
, vol.41
, pp. 388-397
-
-
Privé, G.1
-
3
-
-
79958126240
-
Choosing membrane mimetics for NMR structural studies of transmembrane proteins
-
Warschawski, D. E.; Arnold, A. A.; Beaugrand, M.; Gravel, A.; Chartrand, é.; Marcotte, I.; Chartrand, E. Choosing membrane mimetics for NMR structural studies of transmembrane proteins Biochim. Biophys. Acta: Biomembr. 2011, 1808, 1957-1974
-
(2011)
Biochim. Biophys. Acta: Biomembr.
, vol.1808
, pp. 1957-1974
-
-
Warschawski, D.E.1
Arnold, A.A.2
Beaugrand, M.3
Gravel, A.4
Chartrand, E.5
Marcotte, I.6
Chartrand, E.7
-
4
-
-
0034707086
-
Interaction of membrane proteins and lipids with solubilizing detergents
-
le Maire, M.; Champeil, P.; Moller, J. V.; Møller, J. V. Interaction of membrane proteins and lipids with solubilizing detergents Biochim. Biophys. Acta: Biomembr. 2000, 1508, 86-111
-
(2000)
Biochim. Biophys. Acta: Biomembr.
, vol.1508
, pp. 86-111
-
-
Le Maire, M.1
Champeil, P.2
Moller, J.V.3
Møller, J.V.4
-
5
-
-
0029381531
-
The use of Dodecylphosphocholine micelles in solution NMR
-
Kallick, D. A.; Tessmer, M. R.; Watts, C. R.; Li, C. Y. The use of Dodecylphosphocholine micelles in solution NMR J. Magn. Reson. B 1995, 109, 60-65
-
(1995)
J. Magn. Reson. B
, vol.109
, pp. 60-65
-
-
Kallick, D.A.1
Tessmer, M.R.2
Watts, C.R.3
Li, C.Y.4
-
6
-
-
0031920741
-
Studies of the binding and structure of adrenocorticotropin peptides in membrane mimics by NMR spectroscopy and pulsed-field gradient diffusion
-
Gao, X. F.; Wong, T. C. Studies of the binding and structure of adrenocorticotropin peptides in membrane mimics by NMR spectroscopy and pulsed-field gradient diffusion Biophys. J. 1998, 74, 1871-1888
-
(1998)
Biophys. J.
, vol.74
, pp. 1871-1888
-
-
Gao, X.F.1
Wong, T.C.2
-
7
-
-
82755198034
-
Transverse and tangential orientation of predicted transmembrane fragments 4 and 10 from the human multidrug resistance protein (hMRP1/ABCC1) in membrane mimics
-
de Foresta, B.; Vincent, M.; Garrigos, M.; Gallay, J. Transverse and tangential orientation of predicted transmembrane fragments 4 and 10 from the human multidrug resistance protein (hMRP1/ABCC1) in membrane mimics Eur. Biophys. J. 2011, 40, 1043-1060
-
(2011)
Eur. Biophys. J.
, vol.40
, pp. 1043-1060
-
-
De Foresta, B.1
Vincent, M.2
Garrigos, M.3
Gallay, J.4
-
8
-
-
0037111207
-
Micelle-bound conformation of a hairpin-forming peptide: Combined NMR and molecular dynamics study
-
Dixon, A. M.; Venable, R. M.; Pastor, R. W.; Bull, T. E. Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study Biopolymers 2002, 65, 284-298
-
(2002)
Biopolymers
, vol.65
, pp. 284-298
-
-
Dixon, A.M.1
Venable, R.M.2
Pastor, R.W.3
Bull, T.E.4
-
9
-
-
70349745154
-
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins
-
Kim, H. J.; Howell, S. C.; Van Horn, W. D.; Jeon, Y. H.; Sanders, C. R. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins Prog. Nucl. Magn. Reson. Spectrosc. 2009, 55, 335-360
-
(2009)
Prog. Nucl. Magn. Reson. Spectrosc.
, vol.55
, pp. 335-360
-
-
Kim, H.J.1
Howell, S.C.2
Van Horn, W.D.3
Jeon, Y.H.4
Sanders, C.R.5
-
10
-
-
77950576779
-
Influence of phosphocholine alkyl chain length on peptide-micelle interactions and micellar size and shape
-
Göbl, C.; Dulle, M.; Hohlweg, W.; Grossauer, J.; Falsone, S. F.; Glatter, O.; Zangger, K. Influence of phosphocholine alkyl chain length on peptide-micelle interactions and micellar size and shape J. Phys. Chem. B 2010, 114, 4717-4724
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 4717-4724
-
-
Göbl, C.1
Dulle, M.2
Hohlweg, W.3
Grossauer, J.4
Falsone, S.F.5
Glatter, O.6
Zangger, K.7
-
11
-
-
33751017943
-
Solution structure of amphibian tachykinin perolein bound to DPC micelles
-
Dike, A.; Cowsik, S. M. Solution structure of amphibian tachykinin perolein bound to DPC micelles J. Struct. Biol. 2006, 156, 442-452
-
(2006)
J. Struct. Biol.
, vol.156
, pp. 442-452
-
-
Dike, A.1
Cowsik, S.M.2
-
12
-
-
71649092717
-
α-Helical transmembrane peptides: A "divide and Conquer" approach to membrane proteins
-
Bordag, N.; Keller, S. α-Helical transmembrane peptides: A "Divide and Conquer" approach to membrane proteins Chem. Phys. Lipids 2010, 163, 1-26
-
(2010)
Chem. Phys. Lipids
, vol.163
, pp. 1-26
-
-
Bordag, N.1
Keller, S.2
-
13
-
-
36849088540
-
Solution NMR of membrane proteins in bilayer mimics: Small is beautiful, but sometimes bigger is better
-
Poget, S. F.; Girvin, M. E. Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but sometimes bigger is better Biochim. Biophys. Acta 2007, 1768, 3098-3106
-
(2007)
Biochim. Biophys. Acta
, vol.1768
, pp. 3098-3106
-
-
Poget, S.F.1
Girvin, M.E.2
-
14
-
-
0018798032
-
Physicochemical studies of the protein-lipid interactions in melittin-containing micelles
-
Lauterwein, J.; Bösch, C.; Brown, L. R.; Wüthrich, K. Physicochemical studies of the protein-lipid interactions in melittin-containing micelles Biochim. Biophys. Acta: Biomembr. 1979, 556, 244-264
-
(1979)
Biochim. Biophys. Acta: Biomembr.
, vol.556
, pp. 244-264
-
-
Lauterwein, J.1
Bösch, C.2
Brown, L.R.3
Wüthrich, K.4
-
15
-
-
36049014994
-
Size and shape of detergent micelles determined by small-angle X-ray scattering
-
Lipfert, J.; Columbus, L.; Chu, V. B.; Lesley, S. A.; Doniach, S. Size and shape of detergent micelles determined by small-angle X-ray scattering J. Phys. Chem. B 2007, 111, 12427-12438
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 12427-12438
-
-
Lipfert, J.1
Columbus, L.2
Chu, V.B.3
Lesley, S.A.4
Doniach, S.5
-
16
-
-
0033543147
-
Molecular dynamics simulation of the structure and dynamics of a dodecylphosphocholine micelle in aqueous solution
-
Wymore, T.; Gao, X. F.; Wong, T. C. Molecular dynamics simulation of the structure and dynamics of a dodecylphosphocholine micelle in aqueous solution THEOCHEM 1999, 485-486, 195-210
-
(1999)
THEOCHEM
, vol.485-486
, pp. 195-210
-
-
Wymore, T.1
Gao, X.F.2
Wong, T.C.3
-
17
-
-
0034499269
-
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation
-
Marrink, S.-J.; Tieleman, P. D.; Mark, A. E. Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation J. Phys. Chem. B 2000, 104, 12165-12173
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 12165-12173
-
-
Marrink, S.-J.1
Tieleman, P.D.2
Mark, A.E.3
-
18
-
-
0034229640
-
Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation
-
Tieleman, D. P.; van der Spoel, D.; Berendsen, H. J. C. Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation J. Phys. Chem. B 2000, 104, 6380-6388
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6380-6388
-
-
Tieleman, D.P.1
Van Der Spoel, D.2
Berendsen, H.J.C.3
-
19
-
-
0035954988
-
Dynamics of Ganglioside Headgroup in Lipid Environment: Molecular Dynamics Simulations of GM1 Embedded in Dodecylphosphocholine Micelle
-
Vasudevan, S. V.; Balaji, P. V. Dynamics of Ganglioside Headgroup in Lipid Environment: Molecular Dynamics Simulations of GM1 Embedded in Dodecylphosphocholine Micelle J. Phys. Chem. B 2001, 105, 7033-7041
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 7033-7041
-
-
Vasudevan, S.V.1
Balaji, P.V.2
-
20
-
-
33847010221
-
Quantifying the Hydrophobic Effect. 2. A Computer Simulation-Molecular- Thermodynamic Model for the Micellization of Nonionic Surfactants in Aqueous Solution
-
Stephenson, B. C.; Goldsipe, A.; Beers, K. J.; Blankschtein, D. Quantifying the Hydrophobic Effect. 2. A Computer Simulation-Molecular- Thermodynamic Model for the Micellization of Nonionic Surfactants in Aqueous Solution J. Phys. Chem. B 2007, 111, 1045-1062
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 1045-1062
-
-
Stephenson, B.C.1
Goldsipe, A.2
Beers, K.J.3
Blankschtein, D.4
-
21
-
-
1642485164
-
Coarse Grained Model for Semi quantitative Lipid Simulations
-
Marrink, S.-J.; de Vries, A. H.; Mark, A. E. Coarse Grained Model for Semi quantitative Lipid Simulations J. Phys. Chem. B 2004, 108, 750-760
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 750-760
-
-
Marrink, S.-J.1
De Vries, A.H.2
Mark, A.E.3
-
22
-
-
56749177067
-
Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation
-
Fuzo, C. A.; Castro, J. R. M.; Degreve, L. Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation Genet. Mol. Res. 2008, 7, 986-999
-
(2008)
Genet. Mol. Res.
, vol.7
, pp. 986-999
-
-
Fuzo, C.A.1
Castro, J.R.M.2
Degreve, L.3
-
23
-
-
23844477976
-
Implicit Solvent Simulations of DPC Micelle Formation
-
Lazaridis, T.; Mallik, B.; Y., C.; Chen, Y. Implicit Solvent Simulations of DPC Micelle Formation J. Phys. Chem. B 2005, 109, 15098-15106
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 15098-15106
-
-
Lazaridis, T.1
Mallik, B.2
Chen, Y.3
-
24
-
-
36649010822
-
Multi-Mannosides Based on a Carbohydrate Scaffold; Synthesis, Force Field Development, Molecular Dynamics Studies, and Binding Affinities for Lectin Con A
-
Gouin, S.; Vanquelef, E.; Garcia Fernandez, J. M.; Ortiz Mellet, C.; Dupradeau, F.-Y.; Kovensky, J. Multi-Mannosides Based on a Carbohydrate Scaffold; Synthesis, Force Field Development, Molecular Dynamics Studies, and Binding Affinities for Lectin Con A J. Org. Chem. 2007, 72, 9032-9045
-
(2007)
J. Org. Chem.
, vol.72
, pp. 9032-9045
-
-
Gouin, S.1
Vanquelef, E.2
Garcia Fernandez, J.M.3
Ortiz Mellet, C.4
Dupradeau, F.-Y.5
Kovensky, J.6
-
25
-
-
77954566051
-
The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building
-
Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building Phys. Chem. Chem. Phys. 2010, 12, 7821-7839
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.-Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
26
-
-
84869030919
-
-
Manuscript in preparation, 2012
-
Abel, S.; Lorieau, A.; de Foresta, B.; Dupradeau, F.-Y.; Marchi, M. Molecular dynamics simulations of hMRP1 transmembrane segments in different environments. Manuscript in preparation, 2012.
-
Molecular Dynamics Simulations of hMRP1 Transmembrane Segments in Different Environments
-
-
Abel, S.1
Lorieau, A.2
De Foresta, B.3
Dupradeau, F.-Y.4
Marchi, M.5
-
27
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins Struct. Funct. 2006, 65, 712-725
-
(2006)
Proteins Struct. Funct.
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
28
-
-
84858321169
-
Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids
-
Jämbeck, J. P. M.; Lyubartsev, A. P. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids J. Phys. Chem. B 2012, 116, 3164-3179
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 3164-3179
-
-
Jämbeck, J.P.M.1
Lyubartsev, A.P.2
-
29
-
-
84865101970
-
An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes
-
Jämbeck, J. P. M.; Lyubartsev, A. P. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes J. Chem. Theory Comput. 2012, 8, 2938-2948
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2938-2948
-
-
Jämbeck, J.P.M.1
Lyubartsev, A.P.2
-
30
-
-
84865722478
-
GAFFlipid: A General Amber Force Field for the accurate molecular dynamics simulation of phospholipid
-
Dickson, C. J.; Rosso, L.; Betz, R. M.; Walker, R. C.; Gould, I. R. GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid Soft Matter 2012, 8, 9617-9627
-
(2012)
Soft Matter
, vol.8
, pp. 9617-9627
-
-
Dickson, C.J.1
Rosso, L.2
Betz, R.M.3
Walker, R.C.4
Gould, I.R.5
-
31
-
-
41549149586
-
Biomolecular simulations of membranes: Physical properties from different force fields
-
Siu, S. W. I.; Vácha, R.; Jungwirth, P.; Böckmann, R. A. Biomolecular simulations of membranes: physical properties from different force fields J. Chem. Phys. 2008, 128, 125103
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 125103
-
-
Siu, S.W.I.1
Vácha, R.2
Jungwirth, P.3
Böckmann, R.A.4
-
32
-
-
34547372334
-
Performance of the general amber force field in modeling aqueous POPC membrane bilayers
-
Jójárt, B.; Martinek, T. A. Performance of the general amber force field in modeling aqueous POPC membrane bilayers J. Comput. Chem. 2007, 28, 2051-2058
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 2051-2058
-
-
Jójárt, B.1
Martinek, T.A.2
-
33
-
-
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.; OConnor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types J. Phys. Chem. B 2010, 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
Oconnor, J.W.4
Tobias, D.J.5
Mondragon-Ramirez, C.6
Vorobyov, I.7
MacKerell, A.D.8
Pastor, R.W.9
-
34
-
-
78751664249
-
Molecular simulations of dodecyl-β-maltoside micelles in water: Influence of the headgroup conformation and force field parameters
-
Abel, S.; Dupradeau, F.-Y.; Raman, E. P.; MacKerell, A. D.; Marchi, M. Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters J. Phys. Chem. B 2011, 115, 487-499
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 487-499
-
-
Abel, S.1
Dupradeau, F.-Y.2
Raman, E.P.3
MacKerell, A.D.4
Marchi, M.5
-
35
-
-
39049147617
-
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
-
Kirschner, K. N.; Yongye, B., A.; Tschampel, M., S.; González- Outeiriño, J.; Daniels, R., C.; Lachele Foley, B.; J. Woods, R.; Kirschner, K.; Yongye, A.; Tschampel, S.; Daniels, C. GLYCAM06: A generalizable biomolecular force field. Carbohydrates J. Comput. Chem. 2008, 29, 622-655
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 622-655
-
-
Kirschner, K.N.1
Yongye . B, A.2
Tschampel . M, S.3
González- Outeiriño, J.4
Daniels . R, C.5
Lachele Foley, B.6
Woods R, J.7
Kirschner, K.8
Yongye, A.9
Tschampel, S.10
Daniels, C.11
-
36
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
38
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-11574
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-11574
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
39
-
-
84934440741
-
Comparison of protein force fields for molecular dynamics simulations
-
Guvench, O.; MacKerell, A. D. Comparison of protein force fields for molecular dynamics simulations Methods Mol. Biol. 2008, 443, 63-88
-
(2008)
Methods Mol. Biol.
, vol.443
, pp. 63-88
-
-
Guvench, O.1
MacKerell, A.D.2
-
40
-
-
80051743238
-
Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances
-
Cézard, C.; Trivelli, X.; Aubry, F.; Djedaïni-Pilard, F.; Dupradeau, F.-Y. Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances Phys. Chem. Chem. Phys. 2011, 13, 15103-15121
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 15103-15121
-
-
Cézard, C.1
Trivelli, X.2
Aubry, F.3
Djedaïni-Pilard, F.4
Dupradeau, F.-Y.5
-
41
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
42
-
-
84986516411
-
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
-
Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins J. Comput. Chem. 1995, 16, 1357-1377
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
43
-
-
38549152775
-
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
-
Dupradeau, F.-Y.; Cézard, C.; Lelong, R.; Stanislawiak, é.; Pêcher, J.; Delepine, J. C. R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries Nucleic Acids Res. 2008, D360-D367
-
(2008)
Nucleic Acids Res.
-
-
Dupradeau, F.-Y.1
Cézard, C.2
Lelong, R.3
Stanislawiak, E.4
Pêcher, J.5
Delepine, J.C.6
-
44
-
-
84873055189
-
-
John Wiley and Sons: New York
-
Hehre, W. J.; Radom, L.; Schleyer, P. V.; Pople, J. Ab Initio Molecular Orbital Theory; John Wiley and Sons: New York, 1986; p 576.
-
(1986)
Ab Initio Molecular Orbital Theory
, pp. 576
-
-
Hehre, W.J.1
Radom, L.2
Schleyer, P.V.3
Pople, J.4
-
45
-
-
70450206724
-
-
Revision A.1; Gaussian, Inc: Wallingford, CT
-
Frisch, M. J. G.; Trucks, W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L. Gaussian 09, Revision A.1; Gaussian, Inc: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.G.1
Trucks, W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
Nakatsuji, H.11
Caricato, M.12
Li, X.13
Hratchian, H.P.14
Izmaylov, A.F.15
Bloino, J.16
Zheng, G.17
Sonnenberg, J.L.18
-
46
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M. L. Analytical molecular surface calculation J. Appl. Crystallogr. 1983, 16, 548-558
-
(1983)
J. Appl. Crystallogr.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
47
-
-
79959999377
-
Server: A web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
-
Vanquelef, E.; Simon, S.; Marquant, G.; Garcia, E.; Klimerak, G.; Delepine, J. C.; Cieplak, P.; Dupradeau, F.-Y. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments Nucleic Acids Res. 2011, 39, W511-W517
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Vanquelef, E.1
Simon, S.2
Marquant, G.3
Garcia, E.4
Klimerak, G.5
Delepine, J.C.6
Cieplak, P.7
Dupradeau, F.-Y.R.E.D.8
-
48
-
-
21244467488
-
Validation of the 53A6 GROMOS force field
-
Oostenbrink, C.; Soares, T. A.; van der Vegt, N. F. A.; van Gunsteren, W. F. Validation of the 53A6 GROMOS force field Eur. Biophys. J. 2005, 34, 273-284
-
(2005)
Eur. Biophys. J.
, vol.34
, pp. 273-284
-
-
Oostenbrink, C.1
Soares, T.A.2
Van Der Vegt, N.F.A.3
Van Gunsteren, W.F.4
-
49
-
-
77950590441
-
A new force field for simulating phosphatidylcholine bilayers
-
Poger, D.; Van Gunsteren, W. F.; Mark, A. E. A new force field for simulating phosphatidylcholine bilayers J. Comput. Chem. 2010, 31, 1117-1125
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1117-1125
-
-
Poger, D.1
Van Gunsteren, W.F.2
Mark, A.E.3
-
50
-
-
79959713919
-
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
-
Schmid, N.; Eichenberger, A. P.; Choutko, A.; Riniker, S.; Winger, M.; Mark, A. E.; van Gunsteren, W. F. Definition and testing of the GROMOS force-field versions 54A7 and 54B7 Eur. Biophys. J. 2011, 40, 843-856
-
(2011)
Eur. Biophys. J.
, vol.40
, pp. 843-856
-
-
Schmid, N.1
Eichenberger, A.P.2
Choutko, A.3
Riniker, S.4
Winger, M.5
Mark, A.E.6
Van Gunsteren, W.F.7
-
51
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger, O.; Edholm, O.; Jähnig, F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 1997, 72, 2002-2013
-
(1997)
Biophys. J.
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jähnig, F.3
-
52
-
-
33645941402
-
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W. L.; Tirado-Rives, J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
53
-
-
34547324134
-
Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers
-
Cordomí, A.; Perez, J. J. Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers J. Phys. Chem. B 2007, 111, 7052-7063
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7052-7063
-
-
Cordomí, A.1
Perez, J.J.2
-
54
-
-
33645310406
-
Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides
-
Monticelli, L.; Simões, C.; Belvisi, L.; Colombo, G. Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides J. Phys.: Condens. Matter 2006, 18, S329-S345
-
(2006)
J. Phys.: Condens. Matter
, vol.18
-
-
Monticelli, L.1
Simões, C.2
Belvisi, L.3
Colombo, G.4
-
55
-
-
77749320417
-
An iris-like mechanism of pore dilation in the CorA magnesium transport system
-
Chakrabarti, N.; Neale, C.; Payandeh, J.; Pai, E. F.; Pomès, R. An iris-like mechanism of pore dilation in the CorA magnesium transport system Biophys. J. 2010, 98, 784-792
-
(2010)
Biophys. J.
, vol.98
, pp. 784-792
-
-
Chakrabarti, N.1
Neale, C.2
Payandeh, J.3
Pai, E.F.4
Pomès, R.5
-
56
-
-
79954752757
-
Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study
-
Piñeiro, á.; Bond, P. J.; Khalid, S. Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study Biochim. Biophys. Acta 2011, 1808, 1746-1752
-
(2011)
Biochim. Biophys. Acta
, vol.1808
, pp. 1746-1752
-
-
Piñeiro, A.1
Bond, P.J.2
Khalid, S.3
-
57
-
-
79953898210
-
3pi-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state
-
Schwaiger, C. S.; Bjelkmar, P.; Hess, B.; Lindahl, E. 3pi-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state Biophys. J. 2011, 100, 1446-1454
-
(2011)
Biophys. J.
, vol.100
, pp. 1446-1454
-
-
Schwaiger, C.S.1
Bjelkmar, P.2
Hess, B.3
Lindahl, E.4
-
58
-
-
77950106854
-
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
-
Bjelkmar, P.; Larsson, P.; Cuendet, M. A.; Hess, B.; Lindahl, E. Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models J. Chem. Theory Comput. 2010, 6, 459-466
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 459-466
-
-
Bjelkmar, P.1
Larsson, P.2
Cuendet, M.A.3
Hess, B.4
Lindahl, E.5
-
59
-
-
85047692291
-
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling
-
Sorin, E. J.; Pande, V. S. Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling J. Comput. Chem. 2005, 26, 682-690
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 682-690
-
-
Sorin, E.J.1
Pande, V.S.2
-
60
-
-
0029099308
-
Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane
-
Chiu, S. W.; Clark, M.; Balaji, V.; Subramaniam, S.; Scott, H. L.; Jakobsson, E. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane Biophys. J. 1995, 69, 1230-1245
-
(1995)
Biophys. J.
, vol.69
, pp. 1230-1245
-
-
Chiu, S.W.1
Clark, M.2
Balaji, V.3
Subramaniam, S.4
Scott, H.L.5
Jakobsson, E.6
-
61
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: fast, flexible, and free J. Comput. Chem. 2005, 26, 1701-18
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
62
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
63
-
-
0015222018
-
Studies on phospholipase A and its zymogen from porcine pancreas. 3. Action of the enzyme on short-chain lecithins
-
de Haas, G. H.; Bonsen, P. P.; Pieterson, W. A.; van Deenen, L. L. Studies on phospholipase A and its zymogen from porcine pancreas. 3. Action of the enzyme on short-chain lecithins Biochim. Biophys. Acta 1971, 239, 252-266
-
(1971)
Biochim. Biophys. Acta
, vol.239
, pp. 252-266
-
-
De Haas, G.H.1
Bonsen, P.P.2
Pieterson, W.A.3
Van Deenen, L.L.4
-
64
-
-
33644644163
-
Insertion and Assembly of Membrane Proteins via Simulation
-
Bond, P. J.; Sansom, M. S. P. Insertion and Assembly of Membrane Proteins via Simulation J. Am. Chem. Soc. 2006, 128, 2697-2704
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
65
-
-
10344247720
-
MD Simulations of Spontaneous Membrane Protein/Detergent Micelle Formation
-
Bond, P. J.; Cuthbertson, J. M.; Deol, S. S.; Sansom, M. S. P. MD Simulations of Spontaneous Membrane Protein/Detergent Micelle Formation J. Am. Chem. Soc. 2004, 126, 15948-15949
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 15948-15949
-
-
Bond, P.J.1
Cuthbertson, J.M.2
Deol, S.S.3
Sansom, M.S.P.4
-
66
-
-
22344445910
-
Molecular Dynamics Simulations of the Helical Antimicrobial Peptide Ovispirin-1 in a Zwitterionic Dodecylphosphocholine Micelle: Insights into Host-Cell Toxicity
-
Khandelia, H.; Kaznessis, Y. N. Molecular Dynamics Simulations of the Helical Antimicrobial Peptide Ovispirin-1 in a Zwitterionic Dodecylphosphocholine Micelle: Insights into Host-Cell Toxicity J. Phys. Chem. B 2005, 109, 12990-12996
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 12990-12996
-
-
Khandelia, H.1
Kaznessis, Y.N.2
-
67
-
-
40549132558
-
Molecular Dynamics Simulation and Thermodynamic Modeling of the Self-Assembly of the Triterpenoids Asiatic Acid and Madecassic Acid in Aqueous Solution
-
Stephenson, B. C.; Goldsipe, A.; Blankschtein, D. Molecular Dynamics Simulation and Thermodynamic Modeling of the Self-Assembly of the Triterpenoids Asiatic Acid and Madecassic Acid in Aqueous Solution J. Phys. Chem. B 2008, 112, 2357-2371
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 2357-2371
-
-
Stephenson, B.C.1
Goldsipe, A.2
Blankschtein, D.3
-
68
-
-
79956028024
-
The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of action
-
Chen, R.; Mark, A. E. The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action Eur. Biophys. J. 2011, 40, 545-553
-
(2011)
Eur. Biophys. J.
, vol.40
, pp. 545-553
-
-
Chen, R.1
Mark, A.E.2
-
69
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 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
-
70
-
-
0004067382
-
-
Pullman, B. Reider: Dodrecht
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. In Intermolecular Forces; Pullman, B., Ed.: Reider: Dodrecht, 1981; p 331.
-
(1981)
Intermolecular Forces
, pp. 331
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
-
71
-
-
84986440341
-
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S.; Kollman, P. A. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
72
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 14101-14107
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 14101-14107
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
73
-
-
33845790250
-
Molecular Dynamics Study of Liquid Water
-
Rahman, A.; Stillinger, F. H. Molecular Dynamics Study of Liquid Water J. Chem. Phys. 1971, 55, 3336-3359
-
(1971)
J. Chem. Phys.
, vol.55
, pp. 3336-3359
-
-
Rahman, A.1
Stillinger, F.H.2
-
74
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
75
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nosé, S. A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 1984, 52, 255-268
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
76
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
77
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method Chem. Phys. 1995, 103, 8577-8594
-
(1995)
Chem. Phys.
, vol.103
, pp. 8577-8594
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
78
-
-
4544369164
-
A generalized reaction field method for molecular dynamics simulations
-
Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A generalized reaction field method for molecular dynamics simulations J. Chem. Phys. 1995, 102, 5451-5459
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Van Gunsteren, W.F.4
-
79
-
-
77955135754
-
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
-
Lange, O. F.; van der Spoel, D.; de Groot, B. L. Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data Biochem. J. 2010, 99, 647-655
-
(2010)
Biochem. J.
, vol.99
, pp. 647-655
-
-
Lange, O.F.1
Van Der Spoel, D.2
De Groot, B.L.3
-
80
-
-
38749123962
-
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
-
Hess, B. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation J. Chem. Theory Comput. 2007, 4, 116-122
-
(2007)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
81
-
-
84857761247
-
Atomistic simulations of micellization of sodium hexyl, heptyl, octyl, and nonyl sulfates
-
Sanders, S. A.; Sammalkorpi, M.; Panagiotopoulos, A. Z. Atomistic simulations of micellization of sodium hexyl, heptyl, octyl, and nonyl sulfates J. Phys. Chem. B 2012, 116, 2430-2437
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 2430-2437
-
-
Sanders, S.A.1
Sammalkorpi, M.2
Panagiotopoulos, A.Z.3
-
82
-
-
0033485638
-
Large scale molecular dynamics simulation of self-assembly processes in short and long chain cationic surfactants
-
Maillet, J.-B.; Lachet, V.; Coveney, P. V. Large scale molecular dynamics simulation of self-assembly processes in short and long chain cationic surfactants Phys. Chem. Chem. Phys. 1999, 1, 5277-5290
-
(1999)
Phys. Chem. Chem. Phys.
, vol.1
, pp. 5277-5290
-
-
Maillet, J.-B.1
Lachet, V.2
Coveney, P.V.3
-
83
-
-
72149123675
-
Atomistic simulations of spontaneous formation and structural properties of linoleic acid micelles in water
-
Abel, S.; Attia, J.; Rémita, S.; Marchi, M.; Urbach, W.; Goldmann, M. Atomistic simulations of spontaneous formation and structural properties of linoleic acid micelles in water Chem. Phys. Lett. 2009, 481, 124-129
-
(2009)
Chem. Phys. Lett.
, vol.481
, pp. 124-129
-
-
Abel, S.1
Attia, J.2
Rémita, S.3
Marchi, M.4
Urbach, W.5
Goldmann, M.6
-
84
-
-
77950552018
-
Molecular Dynamics Simulations of Glycocholate-Oleic Acid Mixed Micelle Assembly
-
Turner, D. C.; Yin, F.; Kindt, J. T.; Zhang, H. Molecular Dynamics Simulations of Glycocholate-Oleic Acid Mixed Micelle Assembly Langmuir 2010, 26, 4687-4692
-
(2010)
Langmuir
, vol.26
, pp. 4687-4692
-
-
Turner, D.C.1
Yin, F.2
Kindt, J.T.3
Zhang, H.4
-
85
-
-
56349083191
-
Implicit Solvent Models for Micellization of Ionic Surfactants
-
Jusufi, A.; Hynninen, A.-P.; Panagiotopoulos, A. Z. Implicit Solvent Models for Micellization of Ionic Surfactants J. Phys. Chem. B 2008, 112, 13783-13792
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13783-13792
-
-
Jusufi, A.1
Hynninen, A.-P.2
Panagiotopoulos, A.Z.3
-
86
-
-
0029912748
-
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
87
-
-
45749157286
-
Molecular dynamics simulation of self-assembly of n- decyltrimethylammonium bromide micelles
-
Jorge, M. Molecular dynamics simulation of self-assembly of n-decyltrimethylammonium bromide micelles Langmuir 2008, 24, 5714-25
-
(2008)
Langmuir
, vol.24
, pp. 5714-5725
-
-
Jorge, M.1
-
89
-
-
79960807978
-
Kinetics of thermo-induced micelle-to-vesicle transitions in a catanionic surfactant system investigated by stopped-flow temperature jump
-
Zhang, J.; Liu, S. Kinetics of thermo-induced micelle-to-vesicle transitions in a catanionic surfactant system investigated by stopped-flow temperature jump Phys. Chem. Chem. Phys. 2011, 13, 12545-12553
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 12545-12553
-
-
Zhang, J.1
Liu, S.2
-
91
-
-
74349095210
-
VORO++: A three-dimensional voronoi cell library in C++
-
Rycroft, C. H. VORO++: a three-dimensional voronoi cell library in C++ Chaos 2009, 19, 041111
-
(2009)
Chaos
, vol.19
, pp. 041111
-
-
Rycroft, C.H.1
-
92
-
-
84927514013
-
Nouvelles applications des paramètres continus à la théorie des formes quadratiques
-
Voronoi, G. F. Nouvelles applications des paramètres continus à la théorie des formes quadratiques J. Reine Angew. Math. 1908, 134, 198-287
-
(1908)
J. Reine Angew. Math.
, vol.134
, pp. 198-287
-
-
Voronoi, G.F.1
-
93
-
-
80052614322
-
Volumetric properties of hydrated peptides: Voronoi-Delaunay analysis of molecular simulation runs
-
Voloshin, V. P.; Medvedev, N. N.; Andrews, M. N.; Burri, R. R.; Winter, R.; Geiger, A. Volumetric properties of hydrated peptides: Voronoi-Delaunay analysis of molecular simulation runs J. Phys. Chem. B 2011, 115, 14217-14228
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 14217-14228
-
-
Voloshin, V.P.1
Medvedev, N.N.2
Andrews, M.N.3
Burri, R.R.4
Winter, R.5
Geiger, A.6
-
94
-
-
0029859688
-
Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure
-
Paci, E.; Marchi, M. Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 11609-11614
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 11609-11614
-
-
Paci, E.1
Marchi, M.2
-
95
-
-
0037129516
-
Molecular Dynamics Simulation of Sodium Dodecyl Sulfate Micelle in Water: Micellar Structural Characteristics and Counterion Distribution
-
Bruce, C. D.; Berkowitz, M. L.; Perera, L.; Forbes, M. D. E. Molecular Dynamics Simulation of Sodium Dodecyl Sulfate Micelle in Water: Micellar Structural Characteristics and Counterion Distribution J. Phys. Chem. B 2002, 106, 3788-3793
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 3788-3793
-
-
Bruce, C.D.1
Berkowitz, M.L.2
Perera, L.3
Forbes, M.D.E.4
-
96
-
-
0002566769
-
Isothermal compressibility of cyclohexane-n-decane, cyclohexane-n- dodecane, and cyclohexane-n-tetradecane
-
Aicart, E.; Tardajos, G.; Diaz Pena, M. Isothermal compressibility of cyclohexane-n-decane, cyclohexane-n-dodecane, and cyclohexane-n-tetradecane J. Chem. Eng. Data 1981, 26, 22-26
-
(1981)
J. Chem. Eng. Data
, vol.26
, pp. 22-26
-
-
Aicart, E.1
Tardajos, G.2
Diaz Pena, M.3
-
97
-
-
0003463967
-
-
Carnegie, P. American Petroleum Institute: Pittsburgh, PA, pages
-
Rossini, F. D. In Selected Values of physical Thermodynamic Properties of Hydrocarbons and Related Compounds; Carnegie, P., Ed.; American Petroleum Institute: Pittsburgh, PA, 1953; 1050 pages.
-
(1953)
Selected Values of Physical Thermodynamic Properties of Hydrocarbons and Related Compounds
, pp. 1050
-
-
Rossini, F.D.1
-
98
-
-
33745763431
-
The structure of zwitterionic phosphocholine surfactant monolayers
-
Yaseen, M.; Lu, J. R.; Webster, J. R. P.; Penfold, J. The structure of zwitterionic phosphocholine surfactant monolayers Langmuir 2006, 22, 5825-5832
-
(2006)
Langmuir
, vol.22
, pp. 5825-5832
-
-
Yaseen, M.1
Lu, J.R.2
Webster, J.R.P.3
Penfold, J.4
-
99
-
-
0027997604
-
Conformational changes of the lecithin headgroup in monolayers at the air/water interface
-
Brumm, T.; Naumann, C.; Sackmann, E.; Rennie, A. R.; Thomas, R. K.; Kanellas, D.; Penfold, J.; Bayerl, T. M. Conformational changes of the lecithin headgroup in monolayers at the air/water interface Eur. Biophys. J. 1994, 23, 289-295
-
(1994)
Eur. Biophys. J.
, vol.23
, pp. 289-295
-
-
Brumm, T.1
Naumann, C.2
Sackmann, E.3
Rennie, A.R.4
Thomas, R.K.5
Kanellas, D.6
Penfold, J.7
Bayerl, T.M.8
-
100
-
-
0026031974
-
Structure of an adsorbed dimyristoylphosphatidylcholine bilayer measured with specular reflection of neutrons
-
Johnson, S. J.; Bayerl, T. M.; McDermott, D. C.; Adam, G. W.; Rennie, A. R.; Thomas, R. K.; Sackmann, E. Structure of an adsorbed dimyristoylphosphatidylcholine bilayer measured with specular reflection of neutrons Biophys. J. 1991, 59, 289-294
-
(1991)
Biophys. J.
, vol.59
, pp. 289-294
-
-
Johnson, S.J.1
Bayerl, T.M.2
McDermott, D.C.3
Adam, G.W.4
Rennie, A.R.5
Thomas, R.K.6
Sackmann, E.7
-
101
-
-
3142723209
-
Determination of bilayer thickness and lipid surface area in unilamellar dimyristoylphosphatidylcholine vesicles from small-angle neutron scattering curves: A comparison of evaluation methods
-
Kucerka, N.; Kiselev, M. A.; Balgavý, P. Determination of bilayer thickness and lipid surface area in unilamellar dimyristoylphosphatidylcholine vesicles from small-angle neutron scattering curves: a comparison of evaluation methods Eur. Biophys. J. 2004, 33, 328-334
-
(2004)
Eur. Biophys. J.
, vol.33
, pp. 328-334
-
-
Kucerka, N.1
Kiselev, M.A.2
Balgavý, P.3
-
102
-
-
79955574923
-
-
Schrodinger LLC. Version 1.3r1; DeLano Scientific: San Carlos, CA
-
Schrodinger LLC. The PyMOL Molecular Graphics System, Version 1.3r1; DeLano Scientific: San Carlos, CA, 2010.
-
(2010)
The PyMOL Molecular Graphics System
-
-
-
103
-
-
0017372433
-
Orientation and flexibility of the choline head group in phosphatidylcholine bilayers
-
Seelig, J.; Gally, H.-U.; Wohlgemuth, R. Orientation and flexibility of the choline head group in phosphatidylcholine bilayers Biochim. Biophys. Acta 1977, 467, 109-119
-
(1977)
Biochim. Biophys. Acta
, vol.467
, pp. 109-119
-
-
Seelig, J.1
Gally, H.-U.2
Wohlgemuth, R.3
-
104
-
-
84986483798
-
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
-
Eisenhaber, F.; Lijnzaad, P.; Argos, P.; Sander, C.; Scharf, M. The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies J. Comput. Chem. 1995, 16, 273-284
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 273-284
-
-
Eisenhaber, F.1
Lijnzaad, P.2
Argos, P.3
Sander, C.4
Scharf, M.5
-
105
-
-
0033516705
-
The packing density in proteins: Standard radii and volumes
-
Tsai, J.; Taylor, R.; Chothia, C.; Gerstein, M. The packing density in proteins: standard radii and volumes J. Mol. Biol. 1999, 290, 253-266
-
(1999)
J. Mol. Biol.
, vol.290
, pp. 253-266
-
-
Tsai, J.1
Taylor, R.2
Chothia, C.3
Gerstein, M.4
-
106
-
-
77951251864
-
Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation
-
Poger, D.; Mark, A. E. Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation Proteins 2010, 78, 1163-1174
-
(2010)
Proteins
, vol.78
, pp. 1163-1174
-
-
Poger, D.1
Mark, A.E.2
-
107
-
-
77958105722
-
On the hydration of the phosphocholine headgroup in aqueous solution
-
Foglia, F.; Lawrence, M. J.; Lorenz, C. D.; McLain, S. E. On the hydration of the phosphocholine headgroup in aqueous solution J. Chem. Phys. 2010, 133, 145103
-
(2010)
J. Chem. Phys.
, vol.133
, pp. 145103
-
-
Foglia, F.1
Lawrence, M.J.2
Lorenz, C.D.3
McLain, S.E.4
-
108
-
-
2942585239
-
Hydrogen Bonding Structure and Dynamics of Water at the Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation
-
Lopez, C. F.; Nielsen, S. O.; Klein, M. L.; Moore, P. B. Hydrogen Bonding Structure and Dynamics of Water at the Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation J. Phys. Chem. B 2004, 108, 6603-6610
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6603-6610
-
-
Lopez, C.F.1
Nielsen, S.O.2
Klein, M.L.3
Moore, P.B.4
-
109
-
-
0000112789
-
Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
-
Tieleman, P. D.; Berendsen, H. J. C. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters J. Chem. Phys. 1996, 105, 4871
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 4871
-
-
Tieleman, P.D.1
Berendsen, H.J.C.2
-
110
-
-
0034950798
-
Effects of phospholipid unsaturation on the membrane/water interface: A molecular simulation study
-
Murzyn, K.; Róg, T.; Jezierski, G.; Takaoka, Y.; Pasenkiewicz-Gierula, M. Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study Biophys. J. 2001, 81, 170-183
-
(2001)
Biophys. J.
, vol.81
, pp. 170-183
-
-
Murzyn, K.1
Róg, T.2
Jezierski, G.3
Takaoka, Y.4
Pasenkiewicz-Gierula, M.5
-
111
-
-
0000065270
-
Hydrogen Bonding of Water to Phosphatidylcholine in the Membrane As Studied by a Molecular Dynamics Simulation: Location, Geometry, and Lipid-Lipid Bridging via Hydrogen-Bonded Water
-
Pasenkiewicz-Gierula, M.; Takaoka, Y.; Miyagawa, H.; Kitamura, K.; Kusumi, A. Hydrogen Bonding of Water to Phosphatidylcholine in the Membrane As Studied by a Molecular Dynamics Simulation: Location, Geometry, and Lipid-Lipid Bridging via Hydrogen-Bonded Water J. Phys. Chem. A 1997, 101, 3677-3691
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3677-3691
-
-
Pasenkiewicz-Gierula, M.1
Takaoka, Y.2
Miyagawa, H.3
Kitamura, K.4
Kusumi, A.5
-
112
-
-
0019330575
-
Polar group conformation of phosphatidylcholine. Effect of solvent and aggregation
-
Hauser, H.; Guyer, W.; Pascher, I.; Skrabal, P.; Sundell, S. Polar group conformation of phosphatidylcholine. Effect of solvent and aggregation Biochemistry 1980, 19, 366-373
-
(1980)
Biochemistry
, vol.19
, pp. 366-373
-
-
Hauser, H.1
Guyer, W.2
Pascher, I.3
Skrabal, P.4
Sundell, S.5
-
113
-
-
55649099854
-
Density functional theory-based conformational analysis of a phospholipid molecule (dimyristoyl phosphatidylcholine)
-
Krishnamurty, S.; Stefanov, M.; Mineva, T.; Bégu, S.; Devoisselle, J. M.; Goursot, A.; Zhu, R.; Salahub, D. R. Density functional theory-based conformational analysis of a phospholipid molecule (dimyristoyl phosphatidylcholine) J. Phys. Chem. B 2008, 112, 13433-13442
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13433-13442
-
-
Krishnamurty, S.1
Stefanov, M.2
Mineva, T.3
Bégu, S.4
Devoisselle, J.M.5
Goursot, A.6
Zhu, R.7
Salahub, D.R.8
-
114
-
-
79953048721
-
Headgroup mediated water insertion into the DPPC bilayer: A molecular dynamics study
-
Pandey, P. R.; Roy, S. Headgroup mediated water insertion into the DPPC bilayer: a molecular dynamics study J. Phys. Chem. B 2011, 115, 3155-3163
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 3155-3163
-
-
Pandey, P.R.1
Roy, S.2
-
115
-
-
0025779595
-
Conformational analysis of the polar head group in phosphatidylcholine bilayers: A structural change induced by cations
-
Akutsu, H.; Nagamori, T. Conformational analysis of the polar head group in phosphatidylcholine bilayers: a structural change induced by cations Biochemistry 1991, 30, 4510-4516
-
(1991)
Biochemistry
, vol.30
, pp. 4510-4516
-
-
Akutsu, H.1
Nagamori, T.2
-
116
-
-
0000545128
-
Conformation of the hydrocarbon chains of sodium dodecyl sulfate molecules in micelles: An FTIR study
-
Holler, F.; Callis, J. B. Conformation of the hydrocarbon chains of sodium dodecyl sulfate molecules in micelles: an FTIR study J. Phys. Chem. 1989, 93, 2053-2058
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 2053-2058
-
-
Holler, F.1
Callis, J.B.2
-
117
-
-
15744368593
-
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
-
Klauda, J. B.; Brooks, B. R.; MacKerell, A. D.; Venable, R. M. R. M.; Pastor, R. W.; MacKerell, A. D., Jr. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer J. Phys. Chem. B 2005, 109, 5300-5311
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 5300-5311
-
-
Klauda, J.B.1
Brooks, B.R.2
MacKerell, A.D.3
Venable, R.M.R.M.4
Pastor, R.W.5
Mackerell Jr., A.D.6
-
118
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller, S. E.; Zhang, Y.; Brooks, B. R. Constant pressure molecular dynamics simulation: The Langevin piston method J. Chem. Phys. 1995, 103, 4613-4621
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Brooks, B.R.3
-
119
-
-
0347963579
-
Molecular Dynamics Simulation Analysis of a Sodium Dodecyl Sulfate Micelle in Aqueous Solution: Decreased Fluidity of the Micelle Hydrocarbon Interior
-
MacKerell, A. D., Jr. Molecular Dynamics Simulation Analysis of a Sodium Dodecyl Sulfate Micelle in Aqueous Solution: Decreased Fluidity of the Micelle Hydrocarbon Interior J. Phys. Chem. 1995, 99, 1846-1855
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 1846-1855
-
-
Mackerell Jr., A.D.1
-
120
-
-
0033718963
-
Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties
-
Bogusz, S.; Venable, R.; Pastor, R. W. Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties J. Phys. Chem. B 2000, 104, 5462-5470
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 5462-5470
-
-
Bogusz, S.1
Venable, R.2
Pastor, R.W.3
-
121
-
-
0035822895
-
Molecular Dynamics Study of Spherical Aggregates of Chain Molecules at Different Degrees of Hydrophilicity in Water Solution
-
Sterpone, F.; Briganti, G.; Pierleoni, C. Molecular Dynamics Study of Spherical Aggregates of Chain Molecules at Different Degrees of Hydrophilicity in Water Solution Langmuir 2001, 17, 5103-5110
-
(2001)
Langmuir
, vol.17
, pp. 5103-5110
-
-
Sterpone, F.1
Briganti, G.2
Pierleoni, C.3
|