-
1
-
-
0001636185
-
Chemical potential of hard-sphere fluids by Monte Carlo methods
-
Adams, D. J. 1974. Chemical potential of hard-sphere fluids by Monte Carlo methods. Mol. Phys. 28:1241-1252.
-
(1974)
Mol. Phys.
, vol.28
, pp. 1241-1252
-
-
Adams, D.J.1
-
2
-
-
33744713394
-
Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid
-
Adams, D. J. 1975. Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid. Mol. Phys. 29:307-311.
-
(1975)
Mol. Phys.
, vol.29
, pp. 307-311
-
-
Adams, D.J.1
-
3
-
-
0001655657
-
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
-
Beglov, D., and B. Roux. 1994. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
4
-
-
9544241030
-
Strong forces between hydrophilic macromolecules: Implications in biological systems
-
Ben-Naim, A. 1991. Strong forces between hydrophilic macromolecules: Implications in biological systems. J. Chem. Phys. 95: 8186-8210.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 8186-8210
-
-
Ben-Naim, A.1
-
7
-
-
9544231346
-
Molecular dynamics simulations with first order coupling to a bath of constant chemical potential
-
Beutler, T. C., and W. F. van Gunsteren. 1994. Molecular dynamics simulations with first order coupling to a bath of constant chemical potential. Mol. Simul. 14:21-34.
-
(1994)
Mol. Simul.
, vol.14
, pp. 21-34
-
-
Beutler, T.C.1
Van Gunsteren, W.F.2
-
8
-
-
0028014642
-
Bound water molecules and conformational stabilization help mediate an antigen-antibody association
-
Bhat, T. N., G. A. Bentley, G. Boulot, M. I. Greene, D. Tello, W. D. Acqua, H. Souchon, F. P. Schwarz, R. A. Mariuzza, and R. J. Poljak. 1994. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl. Acad. Sci. USA. 91: 1089-1093.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 1089-1093
-
-
Bhat, T.N.1
Bentley, G.A.2
Boulot, G.3
Greene, M.I.4
Tello, D.5
Acqua, W.D.6
Souchon, H.7
Schwarz, F.P.8
Mariuzza, R.A.9
Poljak, R.J.10
-
9
-
-
0002899271
-
Grand molecular dynamics: A method for open systems
-
Cagin T., and B. M. Pettitt. 1991. Grand molecular dynamics: a method for open systems. Mol. Simul. 6:5-26.
-
(1991)
Mol. Simul.
, vol.6
, pp. 5-26
-
-
Cagin, T.1
Pettitt, B.M.2
-
12
-
-
0025310356
-
DNA recognition by proteins with the helix-turn-helix motif
-
Harrison, S. C., and A. K. Aggarwal. 1990. DNA recognition by proteins with the helix-turn-helix motif. Annu. Rev. Biochem. 59:933-969.
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 933-969
-
-
Harrison, S.C.1
Aggarwal, A.K.2
-
13
-
-
0026045884
-
Molecular dynamics simulations of dinucleoside and dinucleoside-drug crystal hydrates
-
Herzyk, P., J. M. Goodfellow, and S. Neidle. 1991. Molecular dynamics simulations of dinucleoside and dinucleoside-drug crystal hydrates. J. Biomol. Struct. Dyn. 9:363-386.
-
(1991)
J. Biomol. Struct. Dyn.
, vol.9
, pp. 363-386
-
-
Herzyk, P.1
Goodfellow, J.M.2
Neidle, S.3
-
14
-
-
0028955215
-
Hydration of nucleic acid fragments: Comparison of theory and experiment for high resolution crystal structures of RNA, DNA, and DNA-drug complexes
-
Hummer, G., A. E. Garcia, and D. M. Soumpasis. 1995. Hydration of nucleic acid fragments: comparison of theory and experiment for high resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys. J. 68:1639-1652.
-
(1995)
Biophys. J.
, vol.68
, pp. 1639-1652
-
-
Hummer, G.1
Garcia, A.E.2
Soumpasis, D.M.3
-
15
-
-
0025123333
-
The structure of protein-protein recognition sites
-
Janin, J., and C. Chothia. 1990. The structure of protein-protein recognition sites. J. Mol. Biol. 265:16027-16030.
-
(1990)
J. Mol. Biol.
, vol.265
, pp. 16027-16030
-
-
Janin, J.1
Chothia, C.2
-
16
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 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.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
18
-
-
0042610490
-
Energetics and pattern analysis of crystals of proflavine deoxydinucleosite phosphate
-
Kim, K. S., and E. Clementi. 1985a. Energetics and pattern analysis of crystals of proflavine deoxydinucleosite phosphate. J. Am. Chem. Soc. 107:227-234.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 227-234
-
-
Kim, K.S.1
Clementi, E.2
-
19
-
-
0042610489
-
Hydration analysis of the intercalated complex of deoxydinucleosite phosphate and proflavin: Computer simulations
-
Kim, K. S., and E. Clementi. 1985b. Hydration analysis of the intercalated complex of deoxydinucleosite phosphate and proflavin: computer simulations. J. Phys. Chem. 89:3655-3663.
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 3655-3663
-
-
Kim, K.S.1
Clementi, E.2
-
20
-
-
0020953848
-
Networks of water molecules in a proflavine deoxydinucleosite phosphate complex
-
Kim, K. S., G. Corongiu, and E. Clementi. 1983. Networks of water molecules in a proflavine deoxydinucleosite phosphate complex. J. Biomol. Struct. Dyn. 1:263-285.
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 263-285
-
-
Kim, K.S.1
Corongiu, G.2
Clementi, E.3
-
21
-
-
0027918556
-
Water: Now you see it, now you do not
-
Levitt, M., and B. H. Park. 1993. Water: now you see it, now you do not. Structure, 1:223-226.
-
(1993)
Structure
, vol.1
, pp. 223-226
-
-
Levitt, M.1
Park, B.H.2
-
22
-
-
0028144626
-
A connected-cluster of hydration around myoglobin: Correlation between molecular dynamics simulations and experiment
-
Lounnas, V., and B. M. Pettitt. 1994a. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Proteins Struct. Funct. Genet. 18:133-147.
-
(1994)
Proteins Struct. Funct. Genet.
, vol.18
, pp. 133-147
-
-
Lounnas, V.1
Pettitt, B.M.2
-
23
-
-
0027957222
-
Distribution function implied dynamics versus residence times and correlations: Solvation shells of myoglobin
-
Lounnas, V., and B. M. Pettitt. 1994b. Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin. Proteins Struct. Funct. Genet. 18:148-160.
-
(1994)
Proteins Struct. Funct. Genet.
, vol.18
, pp. 148-160
-
-
Lounnas, V.1
Pettitt, B.M.2
-
24
-
-
0000071422
-
A microscopic view of protein solvation
-
Lounnas, V., B. M. Pettitt, L. Findsen, and S. Subramaniam. 1992. A microscopic view of protein solvation. J. Phys. Chem. 96:7157-7159.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 7157-7159
-
-
Lounnas, V.1
Pettitt, B.M.2
Findsen, L.3
Subramaniam, S.4
-
26
-
-
0001639045
-
A cavity biased (T, V, μ) Monte Carlo method for the computer simulation of fluids
-
Mezei, M. 1980. A cavity biased (T, V, μ) Monte Carlo method for the computer simulation of fluids. Mol. Phys. 40:901-906.
-
(1980)
Mol. Phys.
, vol.40
, pp. 901-906
-
-
Mezei, M.1
-
27
-
-
84893016902
-
Grand canonical ensemble Monte Carlo study of dense liquid Lennard-Jones, soft spheres and water
-
erratum: 67: 1207-1208 (1989)
-
Mezei, M. 1987. Grand canonical ensemble Monte Carlo study of dense liquid Lennard-Jones, soft spheres and water. Mol. Phys. 61:565-582; erratum: 67: 1207-1208 (1989).
-
(1987)
Mol. Phys.
, vol.61
, pp. 565-582
-
-
Mezei, M.1
-
28
-
-
84988080188
-
Generic solvent sites in a crystal
-
Mezei, M., and D. L. Beveridge. 1984. Generic solvent sites in a crystal. J. Comp. Chem. 5:523-527.
-
(1984)
J. Comp. Chem.
, vol.5
, pp. 523-527
-
-
Mezei, M.1
Beveridge, D.L.2
-
29
-
-
0020954112
-
Monte Carlo studies on water in the dCpG/proflavin crystal hydrate
-
Mezei, M., D. L. Beveridge, H. M. Berman, J. M. Goodfellow, J. L. Finney, and S. Neidle. 1983. Monte Carlo studies on water in the dCpG/proflavin crystal hydrate. J. Biomol. Struct. Dyn. 1:287-297.
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 287-297
-
-
Mezei, M.1
Beveridge, D.L.2
Berman, H.M.3
Goodfellow, J.M.4
Finney, J.L.5
Neidle, S.6
-
30
-
-
0025854571
-
X-ray crystal structure of the 2 site-specific mutants his35gln and his351eu of azurin from pseudomonas-aeruginosa
-
Nar, H., A. Messerschmidt, R. Huber, M. van de Kamp, and G. W. Canters. 1991. X-ray crystal structure of the 2 site-specific mutants his35gln and his351eu of azurin from pseudomonas-aeruginosa. J. Mol. Biol. 218: 427-447.
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 427-447
-
-
Nar, H.1
Messerschmidt, A.2
Huber, R.3
Van De Kamp, M.4
Canters, G.W.5
-
31
-
-
0019323773
-
Highly structured water network in crystals of a deoxydinucleoside-drug complex
-
Neidle, S., H. M. Berman, and S. H. Shieh. 1980. Highly structured water network in crystals of a deoxydinucleoside-drug complex. Nature (Lond.) 288:129-133.
-
(1980)
Nature (Lond.)
, vol.288
, pp. 129-133
-
-
Neidle, S.1
Berman, H.M.2
Shieh, S.H.3
-
32
-
-
0026326956
-
Protein hydration in aqueous solution
-
Otting, G., E. Liepinsh, and K. Wuthrich. 1991. Protein hydration in aqueous solution. Science. 254:974-980.
-
(1991)
Science
, vol.254
, pp. 974-980
-
-
Otting, G.1
Liepinsh, E.2
Wuthrich, K.3
-
33
-
-
84927489296
-
Direct determination of fluid phase equilibria by simulation in the Gibbs ensemble: A review
-
Panagiotopoulos, A. Z. 1992. Direct determination of fluid phase equilibria by simulation in the Gibbs ensemble: a review. Molec. Simul. 9:1-23.
-
(1992)
Molec. Simul.
, vol.9
, pp. 1-23
-
-
Panagiotopoulos, A.Z.1
-
34
-
-
0001120964
-
Grand canonical Monte Carlo simulation of water positions in crystal hydrates
-
Resat, H., and M. Mezei. 1994. Grand canonical Monte Carlo simulation of water positions in crystal hydrates. J. Am. Chem. Soc. 116: 7451-7452.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 7451-7452
-
-
Resat, H.1
Mezei, M.2
-
35
-
-
0001453671
-
Use of the grand canonical ensemble in potential of mean force calculations
-
Resat, H., M. Mezei, and J. A. McCammon. 1996. Use of the grand canonical ensemble in potential of mean force calculations. J. Phys. Chem. 100:1426-1433.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 1426-1433
-
-
Resat, H.1
Mezei, M.2
McCammon, J.A.3
-
37
-
-
0001981998
-
Hydration of protein secondary structures: The role in protein folding
-
E. Westhof, editor. CRC Press, Boca Raton, FL.
-
Sekharudu, C. Y., and M. Sundaralingam. 1993. Hydration of protein secondary structures: the role in protein folding. In Water and Biological Macromolecules. E. Westhof, editor. CRC Press, Boca Raton, FL. 148-162.
-
(1993)
Water and Biological Macromolecules
, pp. 148-162
-
-
Sekharudu, C.Y.1
Sundaralingam, M.2
-
38
-
-
0018866267
-
The structure of drug-deoxydinucleoside phosphate complex: Generalized conformational behavior of intercalation complexes with RNA and DNA fragments
-
Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. The structure of drug-deoxydinucleoside phosphate complex: generalized conformational behavior of intercalation complexes with RNA and DNA fragments. Nucleic Acids Res. 8:85-97.
-
(1980)
Nucleic Acids Res.
, vol.8
, pp. 85-97
-
-
Shieh, H.S.1
Berman, H.M.2
Dabrow, M.3
Neidle, S.4
-
39
-
-
0025280401
-
Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding
-
Steitz, T. A. 1990. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23:205-280.
-
(1990)
Q. Rev. Biophys.
, vol.23
, pp. 205-280
-
-
Steitz, T.A.1
-
40
-
-
0006613264
-
Molecular dynamics simulation of a deoxydinucleoside-drug intercalation complex: DCpG/proflavin
-
Swaminathan, S., D. L. Beveridge, and H. M. Herman. 1990. Molecular dynamics simulation of a deoxydinucleoside-drug intercalation complex: dCpG/proflavin. J. Phys. Chem. 94:4660-4665.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 4660-4665
-
-
Swaminathan, S.1
Beveridge, D.L.2
Herman, H.M.3
-
41
-
-
36448999143
-
A computer simulation method for the calculation of chemical potentials of liquids and solids using the bicanonical ensemble
-
Swope, W. C., and H. C. Anderson. 1995. A computer simulation method for the calculation of chemical potentials of liquids and solids using the bicanonical ensemble. J. Chem. Phys. 102:2851-2863.
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 2851-2863
-
-
Swope, W.C.1
Anderson, H.C.2
-
42
-
-
0024713705
-
Enzymes work by solvation substitution rather than by desolvation
-
Warshel, A., J. Aqvist, and S. Creighton. 1989a. Enzymes work by solvation substitution rather than by desolvation. Proc. Natl. Acad. Sci. USA. 86:5820-5824.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 5820-5824
-
-
Warshel, A.1
Aqvist, J.2
Creighton, S.3
-
43
-
-
0024538543
-
How do serine proteases really work?
-
Warshel, A., G. Naray-Szabo, F. Sussmann, and J.-K. Hwang. 1989b. How do serine proteases really work? Biochemistry. 28: 3629-3637.
-
(1989)
Biochemistry
, vol.28
, pp. 3629-3637
-
-
Warshel, A.1
Naray-Szabo, G.2
Sussmann, F.3
Hwang, J.-K.4
-
44
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J., P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta Jr., S.7
Weiner, P.8
|