-
1
-
-
33244497652
-
Colloquium: Scaled particle theory and the length scales of hydrophobicity
-
DOI 10.1103/RevModPhys.78.159
-
Ashbaugh, H. S. & Pratt, L. R. 2006 Colloquium: scaled particle theory and the length scales of hydrophobicity. Rev. Mod. Phys. 78, 159-178. (doi:10.1103/RevModPhys.78.159) (Pubitemid 43277183)
-
(2006)
Reviews of Modern Physics
, vol.78
, Issue.1
-
-
Ashbaugh, H.S.1
Pratt, L.R.2
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
doi:10.1063/1.448118
-
Berendsen, H. J., Postma, J. P., van Gunsteren, W. F., DiNola, A. & Haak, J. R. 1984 Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690. (doi:10.1063/ 1.448118)
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.1
Postma, J.P.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
3
-
-
0032540358
-
Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity
-
DOI 10.1006/jmbi.1998.1669
-
Clackson, T., Ultsch, M. H., Wells, J. A. & de Vos, A. M. 1998 Structural and functional analysis of the 1 : 1 growth hormone : receptor complex reveals the molecular basis for receptor affinity. J. Mol. Biol. 277, 1111-1128. (doi: 10.1006/jmbi.1998.1669) (Pubitemid 28190850)
-
(1998)
Journal of Molecular Biology
, vol.277
, Issue.5
, pp. 1111-1128
-
-
Clackson, T.1
Ultsch, M.H.2
Wells, J.A.3
De Vos, A.M.4
-
4
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
doi: 10.1063/1.464397
-
Darden, T., York, D. & Pedersen, L. 1993 Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10 089-10 092. (doi: 10.1063/1.464397)
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
5
-
-
0004240239
-
-
New York, NY: Dover Publications
-
Debye, P. 1929 Polar molecules. New York, NY: Dover Publications.
-
(1929)
Polar Molecules
-
-
Debye, P.1
-
6
-
-
42749102158
-
Dielectric modulation of biological water
-
DOI 10.1103/PhysRevLett.93.228104, 228104
-
Despa, F., Fernández, A. & Berry, R. S. 2004 Dielectric modulation of biological water. Phys. Rev. Lett. 93, 228104. (doi:10.1103/PhysRevLett.93.228104) (Pubitemid 40072813)
-
(2004)
Physical Review Letters
, vol.93
, Issue.22
, pp. 2281041-2281044
-
-
Despa, F.1
Fernandez, A.2
Berry, R.S.3
-
7
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
DOI 10.1093/nar/gkh381
-
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. 2004 PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665-W667. (doi: 10.1093/nar/gkh381) (Pubitemid 38997419)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB SERVER ISS.
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
8
-
-
5144223810
-
Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions
-
DOI 10.1073/pnas.0405573101
-
Fenimore, P. W., Frauenfelder, H., McCammon, B. H. & Young, R. D. 2004 Bulk solvent and hydration-shell fluctuations, similar to a- and ß-fluctuations in glasses, control protein motions and functions. Proc. Natl Acad. Sci. USA 101, 14408-14413. (doi:10.1073/pnas.0405573101) (Pubitemid 39346762)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.40
, pp. 14408-14413
-
-
Fenimore, P.W.1
Frauenfelder, H.2
McMahon, B.H.3
Young, R.D.4
-
9
-
-
65249122552
-
A unified model of protein dynamics
-
doi:10.1073/pnas.0900336106
-
Frauenfelder, H., Chen, G., Berendzen, J., Fenimore, P. W., Jansson, H., McMahon, B. H., Stroe, I. R., Swenson, J. & Young, R. D. 2009 A unified model of protein dynamics. Proc. Natl Acad. Sci. USA 106, 5129-5134. (doi:10.1073/pnas.0900336106)
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 5129-5134
-
-
Frauenfelder, H.1
Chen, G.2
Berendzen, J.3
Fenimore, P.W.4
Jansson, H.5
McMahon, B.H.6
Stroe, I.R.7
Swenson, J.8
Young, R.D.9
-
11
-
-
40649084349
-
Hydrophobicity of protein surfaces: Separating geometry from chemistry
-
DOI 10.1073/pnas.0708088105
-
Giovambattista, N., Lopez, C. F., Rossky, P. J. & Debenedetti, P. G. 2008 Hydrophobicity of protein surfaces: separating geometry from chemistry. Proc. Natl Acad. Sci. USA 105, 2274-2279. (doi:10.1073/pnas.0708088105) (Pubitemid 351520503)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.7
, pp. 2274-2279
-
-
Giovambattista, N.1
Lopez, C.F.2
Rossky, P.J.3
Debenedetti, P.G.4
-
12
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
doi:10.1103/PhysRevA.31.1695
-
Hoover, W. G. 1985 Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31, 1695-1697. (doi:10.1103/PhysRevA.31.1695)
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
13
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
doi: 10.1063/1.445869
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R. W. & Klein, M. L. 1983 Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935. (doi: 10.1063/1.445869)
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
15
-
-
33751415854
-
3D complex: A structural classification of protein complexes
-
DOI 10.1371/journal.pcbi.0020155
-
Levy, E. D., Pereira-Leal, J. B., Chothia, C. & Teichmann, S. A. 2006 3D complex: a structural classification of protein complexes. PLoS Comput. Biol. 2, el55. (doi:10.1371/journal.pcbi.0020155) (Pubitemid 44819926)
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.11
, pp. 1395-1406
-
-
Levy, E.D.1
Pereira-Leal, J.B.2
Chothia, C.3
Teichmann, S.A.4
-
16
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
DOI 10.1007/S008940100045
-
Lindahl, E., Hess, B. & Van der Spoel, D. 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306-317. (doi:10.1007/s008940100045) (Pubitemid 36153547)
-
(2001)
Journal of Molecular Modeling
, vol.7
, Issue.8
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
17
-
-
0011960339
-
Hydrophobicity at small and large length scales
-
doi:10.1021/jp984327m
-
Lum, K., Chandler, D. & Weeks, J. D. 1999 Hydrophobicity at small and large length scales. J. Phys. Chem. B 103, 4570-4577. (doi:10.1021/jp984327m)
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 4570-4577
-
-
Lum, K.1
Chandler, D.2
Weeks, J.D.3
-
18
-
-
0024153562
-
+channels share common features
-
doi:10.1016/0896-6273(88)90156-0
-
+channels share common features. Neuron 1, 997-1001. (doi:10.1016/0896-6273(88)90156-0)
-
(1998)
Neuron
, vol.1
, pp. 997-1001
-
-
MacKinnon, R.1
Reinhart, P.H.2
White, M.M.3
-
19
-
-
0033606250
-
OPLS all-atom model for amines: Resolution of the amine hydration problem
-
DOI 10.1021/ja984106u
-
Rizzo, R. C. & Jorgensen, W. L. 1999 OPLS all-atom model for amines: resolution of the amine hydration problem. J. Am. Chem. Soc. 121, 4827-4836. (doi:10.1021/ja984106u) (Pubitemid 29252636)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.20
, pp. 4827-4836
-
-
Rizzo, R.C.1
Jorgensen, W.L.2
-
21
-
-
0035451052
-
What are the dielectric 'constants' of proteins and how to validate electrostatic models?
-
DOI 10.1002/prot.1106
-
Schutz, C. N. & Warshel, A. 2001 What are the dielectric constants of proteins and how to validate electrostatic models? Proteins Struct. Funct. Genet. 44, 400-417. (doi:10.1002/prot.1106) (Pubitemid 32768578)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.44
, Issue.4
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
22
-
-
7544234545
-
Continuum equations for dielectric response to macro-molecular assemblies at the nano scale
-
DOI 10.1088/0305-4470/37/41/012, PII S0305447004806000
-
Scott, R., Boland, M., Rogale, K. & Fernández, A. 2004 Continuum equations for dielectric response to macromolecular assemblies at the nanoscale. J. Phys. A 37, 9791-9803. (doi:10.1088/0305-4470/37/41/012) (Pubitemid 39453555)
-
(2004)
Journal of Physics A: Mathematical and General
, vol.37
, Issue.41
, pp. 9791-9803
-
-
Scott, R.1
Boland, M.2
Rogale, K.3
Fernandez, A.4
-
23
-
-
34250434907
-
Structure in aqueous solutions of non-polar solutes from the standpoint of scaled-particle theory
-
doi:10.1007/BF00651970
-
Stillinger, F. H. 1973 Structure in aqueous solutions of non-polar solutes from the standpoint of scaled-particle theory. J. Solut. Chem. 2, 141-158. (doi:10.1007/BF00651970)
-
(1973)
J. Solut. Chem.
, vol.2
, pp. 141-158
-
-
Stillinger, F.H.1
-
24
-
-
0031844416
-
Pairwise calculation of protein solvent-accessible surface areas
-
DOI 10.1016/S1359-0278(98)00036-4
-
Street, A. G. & Mayo, S. L. 1998 Pairwise calculation of solvent accessible surface areas. Fold. Des. 3, 253-258. (doi:10.1016/S1359-0278(98) 00036-4) (Pubitemid 28366047)
-
(1998)
Folding and Design
, vol.3
, Issue.4
, pp. 253-258
-
-
Street, A.G.1
Mayo, S.L.2
-
25
-
-
6344260488
-
Fast accurate evaluation of protein solvent exposure
-
DOI 10.1002/prot.20191
-
Zhang, N., Zeng, C. & Wingreen, N. S. 2004 Fast accurate evaluation of protein solvent exposure. Proteins Struct. Funct. Bioinform. 57, 565-576. (doi:10.1002/prot.20191) (Pubitemid 39390811)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.3
, pp. 565-576
-
-
Zhang, N.1
Zeng, C.2
Wingreen, N.S.3
|