-
1
-
-
0029706920
-
The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies d1.3 and d44.1
-
Goldbaum, F., Schwarz, F., Einsenstein, E., Cauerhff, A., Mariuzza, R., and Poljak, R. (1996) The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies d1.3 and d44.1. J. Mol. Recogn., 9, 6-12.
-
(1996)
J. Mol. Recogn.
, vol.9
, pp. 6-12
-
-
Goldbaum, F.1
Schwarz, F.2
Einsenstein, E.3
Cauerhff, A.4
Mariuzza, R.5
Poljak, R.6
-
2
-
-
0032478266
-
Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease
-
Robinson, C. and Sligar, S. (1998) Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc. Natl. Acad. Sci. U.S.A., 95, 2186-2195.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 2186-2195
-
-
Robinson, C.1
Sligar, S.2
-
3
-
-
0037171138
-
Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies
-
Lynch, T. and Sligar, S. (2002) Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies. Biochim. Biophys. Acta, 1595, 277-282.
-
(2002)
Biochim. Biophys. Acta
, vol.1595
, pp. 277-282
-
-
Lynch, T.1
Sligar, S.2
-
4
-
-
0031047683
-
The role of water in protein-DNA interactions
-
Schwabe, J. (1997) The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol., 7, 126-134.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 126-134
-
-
Schwabe, J.1
-
5
-
-
0031790423
-
Thermodynamic analysis of biomolecules: a volumetric approach
-
Chalikian, T. and Breslauer, K. (1998) Thermodynamic analysis of biomolecules: a volumetric approach. Curr. Opin. Struct. Biol., 8, 657-664.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 657-664
-
-
Chalikian, T.1
Breslauer, K.2
-
6
-
-
0026512015
-
Localization of bound water in the solution structure of the immunoglobulin binding domain of streptococcal protein G. Evidence for solvent-induced helical distortion in solution
-
Clore, G. and Gronenborn, A. (1992) Localization of bound water in the solution structure of the immunoglobulin binding domain of streptococcal protein G. Evidence for solvent-induced helical distortion in solution. J. Mol. Biol., 223, 853-856.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 853-856
-
-
Clore, G.1
Gronenborn, A.2
-
7
-
-
0029024850
-
Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition
-
Eisenstein, M. and Shakked, Z. (1995) Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol., 248, 662-678.
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 662-678
-
-
Eisenstein, M.1
Shakked, Z.2
-
8
-
-
0032475964
-
Water molecules in DNA recognition I: Hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy
-
Sunnerhagen, M., Denisov, V., Venu, K., Bonvin, A., Carey, J., Halle, B., and Otting, G. (1998) Water molecules in DNA recognition I: Hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy. J. Mol. Biol., 282, 847-858.
-
(1998)
J. Mol. Biol.
, vol.282
, pp. 847-858
-
-
Sunnerhagen, M.1
Denisov, V.2
Venu, K.3
Bonvin, A.4
Carey, J.5
Halle, B.6
Otting, G.7
-
9
-
-
0033636839
-
Residence times of water molecules in the hydration sites of myoglobin
-
Makarov, V., Andrews, B., Smith, P., and Pettitt, B. (2000) Residence times of water molecules in the hydration sites of myoglobin. Biophys. J., 79, 2966-2974.
-
(2000)
Biophys. J.
, vol.79
, pp. 2966-2974
-
-
Makarov, V.1
Andrews, B.2
Smith, P.3
Pettitt, B.4
-
10
-
-
0029856410
-
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three fv mutants complexed with lysozyme
-
Fields, B., Goldbaum, F., Dall'Acqua, W., Malchiodi, E., Cauerhff, A., Schwarz, F., Ysern, X., Poljak, R., and Mariuzza, R. (1996) Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three fv mutants complexed with lysozyme. Biochemistry, 35, 15494-15503.
-
(1996)
Biochemistry
, vol.35
, pp. 15494-15503
-
-
Fields, B.1
Goldbaum, F.2
Dall'Acqua, W.3
Malchiodi, E.4
Cauerhff, A.5
Schwarz, F.6
Ysern, X.7
Poljak, R.8
Mariuzza, R.9
-
11
-
-
0029822931
-
Mapping hydration water molecules in the hiv-1 protease/dmp323 complex in solution by NMR spectroscopy
-
Wang, Y., Freedberg, D., Grzesiek, S., Torchia, D., Wingfield, P., Kaufman, J., Stahl, S., Chang, C., and Hodge, C.N. (1996) Mapping hydration water molecules in the hiv-1 protease/dmp323 complex in solution by NMR spectroscopy. Biochemistry, 35, 12694-12704.
-
(1996)
Biochemistry
, vol.35
, pp. 12694-12704
-
-
Wang, Y.1
Freedberg, D.2
Grzesiek, S.3
Torchia, D.4
Wingfield, P.5
Kaufman, J.6
Stahl, S.7
Chang, C.8
Hodge, C.N.9
-
12
-
-
0031591393
-
Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity
-
Labeots, L. and Weiss, M. (1997) Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity. J. Mol. Biol., 269, 113-128.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 113-128
-
-
Labeots, L.1
Weiss, M.2
-
13
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W., Chandrasekhar, J., Madura, J., and Klein, M. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekhar, J.2
Madura, J.3
Klein, M.4
-
14
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H., Grigera, J., and Straatsma, T. (1987) The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.1
Grigera, J.2
Straatsma, T.3
-
15
-
-
84988141840
-
Solving the finite difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods
-
Davis, M. and McCammon, J. (1989) Solving the finite difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods. J. Comput. Chem., 10, 386-391.
-
(1989)
J. Comput. Chem.
, vol.10
, pp. 386-391
-
-
Davis, M.1
McCammon, J.2
-
16
-
-
84986486656
-
Rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nichols, A. and Honig, B. (1991) Rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem., 12, 435-445.
-
(1991)
J. Comput. Chem.
, vol.12
, pp. 435-445
-
-
Nichols, A.1
Honig, B.2
-
17
-
-
26844574873
-
Hydration phenomena, classical electrostatics, and the boundary element method
-
Rashin, A. (1990) Hydration phenomena, classical electrostatics, and the boundary element method. J. Phys. Chem., 94, 1725-1733.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 1725-1733
-
-
Rashin, A.1
-
18
-
-
28944448830
-
A smooth solvation potential based on the conductor-like screening model
-
York, D. and Karplus, M. (1999) A smooth solvation potential based on the conductor-like screening model. J. Phys. Chem. A, 103, 11060-11079.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 11060-11079
-
-
York, D.1
Karplus, M.2
-
19
-
-
0001007983
-
Finite element approach to the electrostatics of macromolecules with arbitrary geometries
-
You, T. and Harvey, S. (1993) Finite element approach to the electrostatics of macromolecules with arbitrary geometries. J. Comput. Chem., 14, 484-501.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 484-501
-
-
You, T.1
Harvey, S.2
-
20
-
-
0003396304
-
Encyclopedia of Computational Chemistry
-
John Wiley & Sons, Inc., New York
-
Coalson, R. and Beck, T. (1998) Encyclopedia of Computational Chemistry, vol. 3, John Wiley & Sons, Inc., New York.
-
(1998)
, vol.3
-
-
Coalson, R.1
Beck, T.2
-
21
-
-
0035825993
-
A dielectric continuum molecular dynamics method
-
Marchi, M., Borgis, D., Levy, N., and Ballone, P. (2001) A dielectric continuum molecular dynamics method. J. Chem. Phys., 114, 4377-4385.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 4377-4385
-
-
Marchi, M.1
Borgis, D.2
Levy, N.3
Ballone, P.4
-
22
-
-
0034227821
-
A general treatment of solvent effects based on screened Coulomb potentials
-
Hassan, S., Guarnieri, F., and Mehler, E. (2000) A general treatment of solvent effects based on screened Coulomb potentials. J. Phys. Chem. B, 104, 6478-6489.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6478-6489
-
-
Hassan, S.1
Guarnieri, F.2
Mehler, E.3
-
23
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu, D., Shenkin, P., Hollinger, F., and Still, W. (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A, 101, 3005-3014.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.2
Hollinger, F.3
Still, W.4
-
24
-
-
0033654297
-
Generalized Born models of macromolecular solvation effects
-
Bashford, D. and Case, D. (2000) Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem., 51, 129-152.
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.2
-
25
-
-
0003644127
-
Theory of Simple Liquids
-
Academic Press, London
-
Hansen, J. and McDonald, I. (1989) Theory of Simple Liquids, Academic Press, London.
-
(1989)
-
-
Hansen, J.1
McDonald, I.2
-
26
-
-
0000574454
-
Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion in biomolecules
-
Pettit, B., Karplus, M., and Rossky, P. (1986) Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion in biomolecules. J. Phys. Chem., 90, 6335-6345.
-
(1986)
J. Phys. Chem.
, vol.90
, pp. 6335-6345
-
-
Pettit, B.1
Karplus, M.2
Rossky, P.3
-
27
-
-
0000105585
-
Solvation of complex molecules in a polar liquid: an integral equation theory
-
Beglov, D. and Roux, B. (1996) Solvation of complex molecules in a polar liquid: an integral equation theory. J. Chem. Phys., 104, 8678-8689.
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 8678-8689
-
-
Beglov, D.1
Roux, B.2
-
28
-
-
0031187388
-
Langevin dipoles model for ab initio calculations of chemical processes in solution: parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution
-
Florian, J. and Warshel, A. (1997) Langevin dipoles model for ab initio calculations of chemical processes in solution: parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution. J. Phys. Chem. B, 101, 5583-5595.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5583-5595
-
-
Florian, J.1
Warshel, A.2
-
29
-
-
0031335637
-
Continuum and dipole-lattice models of solvation
-
Papazyan, A. and Warshel, A. (1997) Continuum and dipole-lattice models of solvation. J. Phys. Chem. B, 101, 11254-11264.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 11254-11264
-
-
Papazyan, A.1
Warshel, A.2
-
30
-
-
0000689663
-
Statistical mechanics of a multipolar gas: a lattice field theory approach
-
Coalson, R. and Duncan, A. (1996) Statistical mechanics of a multipolar gas: a lattice field theory approach. J. Phys. Chem. B, 100, 2612-2620.
-
(1996)
J. Phys. Chem. B
, vol.100
, pp. 2612-2620
-
-
Coalson, R.1
Duncan, A.2
-
31
-
-
36549097982
-
Density functional theory of nonuniform polyatomic systems. I. General formulation
-
Chandler, D., McCoy, J., and Singer, S.J. (1986) Density functional theory of nonuniform polyatomic systems. I. General formulation. J. Chem. Phys., 85, 5971-5982.
-
(1986)
J. Chem. Phys.
, vol.85
, pp. 5971-5982
-
-
Chandler, D.1
McCoy, J.2
Singer, S.J.3
-
32
-
-
0002245425
-
Density functionals in the theory of nonuniform fluids
-
in Fundamental of Inhomogeneous Fluids (ed. D. Henderson), Marcel Dekker, New York
-
Evans, R. (1992) Density functionals in the theory of nonuniform fluids, in Fundamental of Inhomogeneous Fluids (ed. D. Henderson), Marcel Dekker, New York, pp. 85-176.
-
(1992)
, pp. 85-176
-
-
Evans, R.1
-
33
-
-
36449003161
-
Nonlinear counterion screening in colloidal suspensions
-
Lowen, H., Hansen, J., and Madden, P. (1993) Nonlinear counterion screening in colloidal suspensions. J. Chem. Phys., 98, 3275-3289.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 3275-3289
-
-
Lowen, H.1
Hansen, J.2
Madden, P.3
-
34
-
-
2542491956
-
A semi-implicit solvent model for the simulation of peptides and proteins
-
Basdevant, N., Borgis, D., and Ha-Duong, T. (2004) A semi-implicit solvent model for the simulation of peptides and proteins. J. Comput. Chem., 25, 1015-1029.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1015-1029
-
-
Basdevant, N.1
Borgis, D.2
Ha-Duong, T.3
-
35
-
-
33846227551
-
Particle-based implicit solvent model for biosimulations: application to proteins and nucleic acids hydration
-
Basdevant, N., Ha-Duong, T., and Borgis, D. (2006) Particle-based implicit solvent model for biosimulations: application to proteins and nucleic acids hydration. J. Chem. Theory Comput., 2, 1646-1656.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1646-1656
-
-
Basdevant, N.1
Ha-Duong, T.2
Borgis, D.3
-
36
-
-
58049164909
-
A polarizable coarse-grained water model for coarse-grained proteins simulations
-
Ha-Duong, T., Basdevant, N., and Borgis, D. (2009) A polarizable coarse-grained water model for coarse-grained proteins simulations. Chem. Phys. Lett., 468, 79-82.
-
(2009)
Chem. Phys. Lett.
, vol.468
, pp. 79-82
-
-
Ha-Duong, T.1
Basdevant, N.2
Borgis, D.3
-
37
-
-
34548020295
-
A coarse-grained protein-protein potential derived from an all-atom force field
-
Basdevant, N., Borgis, D., and Ha-Duong, T. (2007) A coarse-grained protein-protein potential derived from an all-atom force field. J. Phys. Chem. B, 111, 9390-9399.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 9390-9399
-
-
Basdevant, N.1
Borgis, D.2
Ha-Duong, T.3
-
38
-
-
0037043433
-
Electrostatics on particles: phenomenological and orientational density functional theory approach
-
Ha-Duong, T., Phan, S., Marchi, M., and Borgis, D. (2002) Electrostatics on particles: phenomenological and orientational density functional theory approach. J. Chem. Phys., 117, 541-556.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 541-556
-
-
Ha-Duong, T.1
Phan, S.2
Marchi, M.3
Borgis, D.4
-
39
-
-
0009869207
-
Electrostatic free energy and other properties of states having nonequilibrium polarization. I
-
Marcus, R. (1956) Electrostatic free energy and other properties of states having nonequilibrium polarization. I. J. Chem. Phys., 24, 979-989.
-
(1956)
J. Chem. Phys.
, vol.24
, pp. 979-989
-
-
Marcus, R.1
-
40
-
-
0003699033
-
The Feynman Lectures on Physics: Mainly Electromagnetism and Matter
-
Addison-Wesley, Reading, MA
-
Feynman, R. (1964) The Feynman Lectures on Physics: Mainly Electromagnetism and Matter, Addison-Wesley, Reading, MA.
-
(1964)
-
-
Feynman, R.1
-
41
-
-
0004179874
-
Classical Electrodynamics
-
John Wiley & Sons, Inc., New York
-
Jackson, W. (1999) Classical Electrodynamics, John Wiley & Sons, Inc., New York.
-
(1999)
-
-
Jackson, W.1
-
42
-
-
0009989494
-
Electrostatic models in the theory of solutions
-
Kharkats, Y., Kornyshev, A., and Vorotyntsev, M. (1976) Electrostatic models in the theory of solutions. J. Chem. Soc., Faraday Trans. 2, 72, 361-371.
-
(1976)
J. Chem. Soc., Faraday Trans. 2
, vol.72
, pp. 361-371
-
-
Kharkats, Y.1
Kornyshev, A.2
Vorotyntsev, M.3
-
43
-
-
0037991000
-
Classical solvent dynamics and electron transfer. 1. Continuum theory
-
Calef, D. and Wolynes, P. (1983) Classical solvent dynamics and electron transfer. 1. Continuum theory. J. Phys. Chem., 87, 3387-3400.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 3387-3400
-
-
Calef, D.1
Wolynes, P.2
-
44
-
-
36549103488
-
Solution reaction path hamiltonian for reactions in polar solvents
-
Lee, S. and Hynes, J. (1988) Solution reaction path hamiltonian for reactions in polar solvents. J. Chem. Phys., 88, 6853-6862.
-
(1988)
J. Chem. Phys.
, vol.88
, pp. 6853-6862
-
-
Lee, S.1
Hynes, J.2
-
45
-
-
0025661993
-
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
-
Schaefer, M. and Froemmel, C. (1990) A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J. Mol. Biol., 216, 1045-1066.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 1045-1066
-
-
Schaefer, M.1
Froemmel, C.2
-
46
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer, M. and Karplus, M. (1996) A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem., 100, 1578-1599.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
47
-
-
20644431615
-
Theory of solutions of molecules containing widely separated charges with special application to zwitterions
-
Kirkwood, J. (1934) Theory of solutions of molecules containing widely separated charges with special application to zwitterions. J. Chem. Phys., 2, 351-361.
-
(1934)
J. Chem. Phys.
, vol.2
, pp. 351-361
-
-
Kirkwood, J.1
-
48
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W., Cieplak, P., Bayly, C., Gould, I., Merz, K. Jr, Ferguson, D., Spellmeyer, D., Fox, T., Caldwell, J., and Kollman, P. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.1
Cieplak, P.2
Bayly, C.3
Gould, I.4
Merz Jr., K.5
Ferguson, D.6
Spellmeyer, D.7
Fox, T.8
Caldwell, J.9
Kollman, P.10
-
49
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. Jr, Bashford, D., Bellott, M., Dunbrack, R. Jr, Evanseck, J., Field, M., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F., Mattos, C., Michnick, S., Ngo, T., Nguyen, D., Prodhom, B., Reiher, W. III, Roux, B., Schlenkrich, M., Smith, J., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.18
Prodhom, B.19
Reiher III, W.20
Roux, B.21
Schlenkrich, M.22
Smith, J.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
50
-
-
0017100947
-
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A. and Levitt, M. (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol., 103, 227-249.
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
51
-
-
0021476470
-
Calculations of electrostatic interactions in biological systems and in solutions
-
Warshel, A. and Russell, S. (1984) Calculations of electrostatic interactions in biological systems and in solutions. Q. Rev. Biophys., 17, 283-422.
-
(1984)
Q. Rev. Biophys.
, vol.17
, pp. 283-422
-
-
Warshel, A.1
Russell, S.2
-
52
-
-
33846217411
-
Static dielectric properties of Stockmayer fluids
-
Pollock, E. and Alder, B. (1980) Static dielectric properties of Stockmayer fluids. Physica, 102A, 1-21.
-
(1980)
Physica
, vol.102 A
, pp. 1-21
-
-
Pollock, E.1
Alder, B.2
-
53
-
-
0014665094
-
Phase transitions of the Lennard-Jones system
-
Hansen, J. and Verlet, L. (1969) Phase transitions of the Lennard-Jones system. Phys. Rev., 184, 151-161.
-
(1969)
Phys. Rev.
, vol.184
, pp. 151-161
-
-
Hansen, J.1
Verlet, L.2
-
54
-
-
46149104297
-
Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor
-
Masella, M., Borgis, D., and Cuniasse, P. (2008) Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor. J. Comput. Chem., 29, 1707-1724.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1707-1724
-
-
Masella, M.1
Borgis, D.2
Cuniasse, P.3
-
55
-
-
34250928962
-
Volumen und Hydratationswarme der Ionen
-
Born, M. (1920) Volumen und Hydratationswarme der Ionen. Z. Phys., 1, 45-48.
-
(1920)
Z. Phys.
, vol.1
, pp. 45-48
-
-
Born, M.1
-
56
-
-
0010262629
-
ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions
-
Procacci, P., Darden, T., Paci, E., and Marchi, M. (1997) ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions. J. Comput. Chem., 18, 1848-1862.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1848-1862
-
-
Procacci, P.1
Darden, T.2
Paci, E.3
Marchi, M.4
-
57
-
-
0000504254
-
A multiple-time-step molecular dynamics algorithm for macromolecules
-
Humphreys, D., Friesner, R., and Berne, B. (1994) A multiple-time-step molecular dynamics algorithm for macromolecules. J. Phys. Chem., 98, 6885-6892.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 6885-6892
-
-
Humphreys, D.1
Friesner, R.2
Berne, B.3
-
58
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nose, S. (1984) A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys., 81, 511-519.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nose, S.1
-
59
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Rickaert, J., Ciccotti, G., and Berendsen, H. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys., 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Rickaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
60
-
-
0023122030
-
Tests of the helix dipole model for stabilization of alpha-helices
-
Shoemaker, K., Kim, P., York, E., Stewart, J., and Baldwin, R. (1987) Tests of the helix dipole model for stabilization of alpha-helices. Nature, 326, 563-567.
-
(1987)
Nature
, vol.326
, pp. 563-567
-
-
Shoemaker, K.1
Kim, P.2
York, E.3
Stewart, J.4
Baldwin, R.5
-
61
-
-
0024472052
-
Proton NMR studies of the solution conformations of an analog of the C-peptide of ribonuclease A
-
Osterhout, J.J. Jr, Baldwin, R.L., York, E.J., Stewart, J.M., Dyson, H.J., and Wright, P.E. (1989) Proton NMR studies of the solution conformations of an analog of the C-peptide of ribonuclease A. Biochemistry, 28, 7059-7064.
-
(1989)
Biochemistry
, vol.28
, pp. 7059-7064
-
-
Osterhout Jr., J.J.1
Baldwin, R.L.2
York, E.J.3
Stewart, J.M.4
Dyson, H.J.5
Wright, P.E.6
-
63
-
-
0028986918
-
Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations
-
Smith, P.E., van Schaik, R.C., Szyperski, T., Wüthrich, K., and van Gunsteren, W. (1995) Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. J. Mol. Biol., 246, 356-365.
-
(1995)
J. Mol. Biol.
, vol.246
, pp. 356-365
-
-
Smith, P.E.1
Van Schaik, R.C.2
Szyperski, T.3
Wüthrich, K.4
Van Gunsteren, W.5
-
64
-
-
0028805413
-
Extensive nonrandom structure in reduced and unfold bovine pancreatic trypsin inhibitor
-
Pan, H., Barbar, E., Barany, G., and Woodward, C. (1995) Extensive nonrandom structure in reduced and unfold bovine pancreatic trypsin inhibitor. Biochemistry, 34, 13974-13981.
-
(1995)
Biochemistry
, vol.34
, pp. 13974-13981
-
-
Pan, H.1
Barbar, E.2
Barany, G.3
Woodward, C.4
-
65
-
-
0028787226
-
Structural and dynamics characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy
-
Frank, M., Clore, G., and Gronenbron, A. (1995) Structural and dynamics characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci., 4, 2605-2615.
-
(1995)
Protein Sci.
, vol.4
, pp. 2605-2615
-
-
Frank, M.1
Clore, G.2
Gronenbron, A.3
-
66
-
-
0034733005
-
Role of sidechains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G
-
Kobayashi, N., Honda, S., Yoshii, H., and Munekata, E. (2000) Role of sidechains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G. Biochemistry, 39, 6564-6571.
-
(2000)
Biochemistry
, vol.39
, pp. 6564-6571
-
-
Kobayashi, N.1
Honda, S.2
Yoshii, H.3
Munekata, E.4
-
67
-
-
0034636847
-
Synthesis and characterization of a beta-hairpin peptide that represents a core module of bovine pancreatic trypsin inhibitor (BPTI)
-
Carulla, N., Woodward, C., and Barany, G. (2000) Synthesis and characterization of a beta-hairpin peptide that represents a core module of bovine pancreatic trypsin inhibitor (BPTI). Biochemistry, 39, 7927-7937.
-
(2000)
Biochemistry
, vol.39
, pp. 7927-7937
-
-
Carulla, N.1
Woodward, C.2
Barany, G.3
-
68
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker, N., Sept, D., Joseph, S., Holst, M., and McCammon, J. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U.S.A., 98, 10037-10041.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.1
Sept, D.2
Joseph, S.3
Holst, M.4
McCammon, J.5
-
69
-
-
0030862276
-
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions and solvation
-
Young, M., Ravishanker, G., and Beveridge, D. (1997) A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions and solvation. Biophys. J., 73, 2313-2336.
-
(1997)
Biophys. J.
, vol.73
, pp. 2313-2336
-
-
Young, M.1
Ravishanker, G.2
Beveridge, D.3
-
70
-
-
0029776466
-
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations
-
Auffinger, P. and Westhof, E. (1996) H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys. J., 71, 940-954.
-
(1996)
Biophys. J.
, vol.71
, pp. 940-954
-
-
Auffinger, P.1
Westhof, E.2
-
71
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery, R. and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam., 6, 63-91.
-
(1988)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
72
-
-
0029941154
-
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham, T. III and Kollman, P. (1996) Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol., 259, 434-444.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 434-444
-
-
Cheatham III, T.1
Kollman, P.2
-
73
-
-
0034615785
-
An A-type double helix of DNA having B-type puckering of the deoxyribose rings
-
Trantirek, L., Stefl, R., Vorlickova, M., Koca, J., Sklenar, V., and Kypr, J. (2000) An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J. Mol. Biol., 297, 907-922.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 907-922
-
-
Trantirek, L.1
Stefl, R.2
Vorlickova, M.3
Koca, J.4
Sklenar, V.5
Kypr, J.6
-
74
-
-
0036286851
-
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment
-
Makarov, V., Pettitt, B., and Feig, M. (2002) Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Accts. Chem. Res., 35, 376-384.
-
(2002)
Accts. Chem. Res.
, vol.35
, pp. 376-384
-
-
Makarov, V.1
Pettitt, B.2
Feig, M.3
|