-
1
-
-
0018094892
-
Electrostatic effects in proteins
-
Perutz, M. Electrostatic effects in proteins. Science 1978, 201, 1187-1191.
-
(1978)
Science
, vol.201
, pp. 1187-1191
-
-
Perutz, M.1
-
2
-
-
0021476470
-
Calculations of electrostatic effects in biological systems and in solutions
-
Warshel, A.; Russell, S. Calculations of electrostatic effects in biological systems and in solutions. Q. Rev. Biophys. 1984, 17, 283-342.
-
(1984)
Q. Rev. Biophys.
, vol.17
, pp. 283-342
-
-
Warshel, A.1
Russell, S.2
-
3
-
-
0031776357
-
Electrostatic contributions to molecular free energies in solution
-
Schaefer, M.; Vlijmen, H. v.; Karplus, M. Electrostatic contributions to molecular free energies in solution. Adv. Prot. Chem. 1998, 51, 1-57.
-
(1998)
Adv. Prot. Chem.
, vol.51
, pp. 1-57
-
-
Schaefer, M.1
Vlijmen, H.V.2
Karplus, M.3
-
4
-
-
0037529067
-
Electrostatics and dynamics of proteins
-
Simonson, T. Electrostatics and dynamics of proteins. Rep. Prog. Phys. 2003, 66, 737-787.
-
(2003)
Rep. Prog. Phys.
, vol.66
, pp. 737-787
-
-
Simonson, T.1
-
5
-
-
0023645765
-
Prediction of electrostatic effects of engineering of protein charges
-
Sternberg, M.; Hayes, F.; Russell, A.; Thomas, P.; Fersht, A. Prediction of electrostatic effects of engineering of protein charges. Nature 1987, 330, 86-88.
-
(1987)
Nature
, vol.330
, pp. 86-88
-
-
Sternberg, M.1
Hayes, F.2
Russell, A.3
Thomas, P.4
Fersht, A.5
-
6
-
-
0024495355
-
Effects of buried ionizable amino acids on the reduction potential of recombinant hemoglobin
-
Varadarajan, R.; Zewert, T.; Gray, H.; Boxer, S. Effects of buried ionizable amino acids on the reduction potential of recombinant hemoglobin. Science 1989, 243, 69-72.
-
(1989)
Science
, vol.243
, pp. 69-72
-
-
Varadarajan, R.1
Zewert, T.2
Gray, H.3
Boxer, S.4
-
7
-
-
1842513901
-
On intermolecular and intramolecular interactions between independent pairs of binding sites in proteins and other molecules
-
Hill, T. On intermolecular and intramolecular interactions between independent pairs of binding sites in proteins and other molecules. J. Am. Chem. Soc. 1956, 78, 5529.
-
(1956)
J. Am. Chem. Soc.
, vol.78
, pp. 5529
-
-
Hill, T.1
-
8
-
-
73649156890
-
Physical principles in the construction of regular viruses
-
Caspar, D.; Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quantum Biol. 1962, 27, 1-24.
-
(1962)
Cold Spring Harbor Symp. Quantum Biol.
, vol.27
, pp. 1-24
-
-
Caspar, D.1
Klug, A.2
-
9
-
-
0023645866
-
What about protein polarity?
-
Warshel, A. What about protein polarity? Nature 1987, 330, 15-17.
-
(1987)
Nature
, vol.330
, pp. 15-17
-
-
Warshel, A.1
-
10
-
-
33947468892
-
Theory of protein titration curves. General equations for impenetrable spheres
-
Tanford, C.; Kirkwood, J. Theory of protein titration curves. General equations for impenetrable spheres. J. Am. Chem. Soc. 1957, 79, 5333-5339.
-
(1957)
J. Am. Chem. Soc.
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.2
-
12
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
Elcock, A. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 2001, 312, 885-896.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 885-896
-
-
Elcock, A.1
-
13
-
-
0035940421
-
THEMATICS a simple computational predictor of enzyme function from structure
-
Ondrechen, M.; Clifton, J.; Ringe, D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 12473-12478.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.1
Clifton, J.2
Ringe, D.3
-
14
-
-
0028983852
-
Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution
-
Simonson, T.; Perahia, D. Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution. J. Am. Chem. Soc. 1995, 117, 7987-8000.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 7987-8000
-
-
Simonson, T.1
Perahia, D.2
-
15
-
-
0009517080
-
What are the dielectric 'constants' of proteins and how to validate electrostatic models?
-
Schutz, C.; Warshel, A. What are the dielectric 'constants' of proteins and how to validate electrostatic models? Proteins 2001, 8, 211-217.
-
(2001)
Proteins
, vol.8
, pp. 211-217
-
-
Schutz, C.1
Warshel, A.2
-
17
-
-
0025718561
-
a of 7.5. Its titration produces a related shift in global stability
-
a of 7.5. Its titration produces a related shift in global stability. Biochemistry 1991, 30, 7603-7609.
-
(1991)
Biochemistry
, vol.30
, pp. 7603-7609
-
-
Langsetmo, K.1
Fuchs, J.2
Woodward, C.3
-
19
-
-
0030050327
-
Characterization of the pH titration shifts of ribonuclease A by one and two-dimensional nuclear magnetic resonanee spectroscopy
-
Baker, W.; Kintanar, A. Characterization of the pH titration shifts of ribonuclease A by one and two-dimensional nuclear magnetic resonanee spectroscopy. Arch. Biochem. Biophys. 1996, 327, 189-199.
-
(1996)
Arch. Biochem. Biophys.
, vol.327
, pp. 189-199
-
-
Baker, W.1
Kintanar, A.2
-
20
-
-
0035957234
-
A novel view of pH titration in biomolecules
-
Onufriev, A.; Case, D.; Ullmann, M. A novel view of pH titration in biomolecules. Biochemistry 2001, 40, 3413-3419.
-
(2001)
Biochemistry
, vol.40
, pp. 3413-3419
-
-
Onufriev, A.1
Case, D.2
Ullmann, M.3
-
21
-
-
0025197061
-
a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
-
a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990, 29, 10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
22
-
-
0028305457
-
Prediction of pH dependent properties of proteins
-
Antosiewicz, J.; McCammon, J.; Gilson, M. Prediction of pH dependent properties of proteins. J. Mol. Biol. 1994, 238, 415-436.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 415-436
-
-
Antosiewicz, J.1
McCammon, J.2
Gilson, M.3
-
23
-
-
33748593093
-
a's of ionizable groups in proteins
-
a's of ionizable groups in proteins. J. Phys. Chem. 1996. 100, 17373-17387.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 17373-17387
-
-
Demchuk, E.1
Wade, R.2
-
24
-
-
0033613164
-
Tanlord-Kirkwood electrostatics for protein modeling
-
Havranek, J.; Harbury, P. Tanlord-Kirkwood electrostatics for protein modeling. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11145-11150.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 11145-11150
-
-
Havranek, J.1
Harbury, P.2
-
27
-
-
0032516494
-
a's in the active site of Escherichia coli thioredoxin
-
a's in the active site of Escherichia coli thioredoxin. Biochemistry 1998, 37, 10298-10306.
-
(1998)
Biochemistry
, vol.37
, pp. 10298-10306
-
-
Dillet, V.1
Dyson, J.2
Bashford, D.3
-
28
-
-
0000671518
-
a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches
-
a's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J. Phys. Chem. B 1997, 101, 4458-4472.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 4458-4472
-
-
Sham, Y.1
Chu, Z.2
Warshel, A.3
-
29
-
-
0000875502
-
A Poisson-Boltzmann study of charge insertion in an enzyme active site: The effect of dielectric relaxation
-
Simonson, T.; Archontis, G.; Karplus, M. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation. J. Phys. Chem. B 1999, 103, 6142-6156.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 6142-6156
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
30
-
-
0035823823
-
Dielectric relaxation in an enzyme active site: Molecular dynamics simulations intepreted with a macroscopic continuum model
-
Archontis, G.; Simonson, T. Dielectric relaxation in an enzyme active site: molecular dynamics simulations intepreted with a macroscopic continuum model. J. Am. Chem. Soc. 2001, 123, 11047-11056.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 11047-11056
-
-
Archontis, G.1
Simonson, T.2
-
31
-
-
0023060081
-
Free energy changes in solvated proteins: Microscopic calculations using a reversible charging process
-
Warshel, A.; Sussman, F.; King, G. Free energy changes in solvated proteins: microscopic calculations using a reversible charging process. Biochemstry 1986, 25, 8368-8372.
-
(1986)
Biochemstry
, vol.25
, pp. 8368-8372
-
-
Warshel, A.1
Sussman, F.2
King, G.3
-
32
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman, P. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395
-
-
Kollman, P.1
-
33
-
-
0041754408
-
Free energy calculations
-
O. Becker. A. Mackerell, Jr.; B. Roux: M. Watanabe, Eds. Marcel Dekker: NY. ch. 9
-
Simonson, T. Free energy calculations. In Computational Biochemistry & Biophysics O. Becker. A. Mackerell, Jr.; B. Roux: M. Watanabe, Eds. Marcel Dekker: NY. 2001. ch. 9.
-
(2001)
Computational Biochemistry & Biophysics
-
-
Simonson, T.1
-
34
-
-
0032054517
-
Electrostatic effects in macromolecules: Fundamental concepts and practical modelling
-
Warshel, A.; Papazyan, A. Electrostatic effects in macromolecules: fundamental concepts and practical modelling. Curr. Op. Struct Biol. 1998, 8, 211-217.
-
(1998)
Curr. Op. Struct Biol.
, vol.8
, pp. 211-217
-
-
Warshel, A.1
Papazyan, A.2
-
35
-
-
0033012333
-
A self-consistent, microenvironmet modulated screened Coulomb potential approximation to calculate pH-dependent effects in proteins
-
Mehler, E.; Guarneri, F. A self-consistent, microenvironmet modulated screened Coulomb potential approximation to calculate pH-dependent effects in proteins. Biophys. J. 1999, 77, 3-22.
-
(1999)
Biophys. J.
, vol.77
, pp. 3-22
-
-
Mehler, E.1
Guarneri, F.2
-
37
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
38
-
-
0033024177
-
Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
-
Sagui, C.; Darden, T. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
-
(1999)
Annu. Rev. Biophys. Biomol. Struct.
, vol.28
, pp. 155-179
-
-
Sagui, C.1
Darden, T.2
-
40
-
-
0028859420
-
Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
-
You, T.; Bashford, D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys. J. 1995, 69, 1721-1733.
-
(1995)
Biophys. J.
, vol.69
, pp. 1721-1733
-
-
You, T.1
Bashford, D.2
-
41
-
-
33748400070
-
Including side chain flexibility in continuum electrostatic calculations of protein titration
-
Beroza, P.; Case, D. Including side chain flexibility in continuum electrostatic calculations of protein titration. J. Phys. Chem. 1996, 100, 20156-20163.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 20156-20163
-
-
Beroza, P.1
Case, D.2
-
42
-
-
0033614791
-
B in bacterial photosynthetic reaction centers
-
B in bacterial photosynthetic reaction centers. Biochemistry 1999, 38, 8253-8270.
-
(1999)
Biochemistry
, vol.38
, pp. 8253-8270
-
-
Alexov, E.1
Gunner, M.2
-
43
-
-
0001585447
-
Computation of electrostatic forces on solvated molecules using the Poison-Boltzmann equation
-
Gilson, M.; Davis, M.; Luty, B.; McCammon, J. Computation of electrostatic forces on solvated molecules using the Poison-Boltzmann equation. J. Phys. Chem. 1993, 97, 3591-3600.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 3591-3600
-
-
Gilson, M.1
Davis, M.2
Luty, B.3
McCammon, J.4
-
44
-
-
0032096837
-
Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
-
Im, W.; Beglov, D.; Roux, B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput. Phys. Comm. 1998, 111, 59-75.
-
(1998)
Comput. Phys. Comm.
, vol.111
, pp. 59-75
-
-
Im, W.1
Beglov, D.2
Roux, B.3
-
45
-
-
0035825993
-
A dielectric continuum molecular dynamics method
-
M. Marchi and D. Borgis and N. Levy and P. Ballone. A dielectric continuum molecular dynamics method. J. Chem. Phys. 2001, 114, 4327-4385.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 4327-4385
-
-
Marchi, M.1
Borgis, D.2
Levy, N.3
Ballone, P.4
-
46
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C.; Tempczyk, A.; Hawley, R.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.3
Hendrickson, T.4
-
47
-
-
0033654297
-
Generalized Born models of macromolecular solvation effects
-
Bashford, D.; Case, D. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.2
-
48
-
-
0037653179
-
A fast and general continuum approach for describing electrostatic effects in molecular dynamics simulations of biomolecules
-
Hassan, S.; Zhang, D.; Mehler, E.; Weinstein, H. A fast and general continuum approach for describing electrostatic effects in molecular dynamics simulations of biomolecules. Biophys. J. 2002, 82, 2363.
-
(2002)
Biophys. J.
, vol.82
, pp. 2363
-
-
Hassan, S.1
Zhang, D.2
Mehler, E.3
Weinstein, H.4
-
49
-
-
4043132337
-
Constant pH molecular dynamics using continuous titration coordinates
-
in press
-
Lee, M.; Salsbury Jr.; F.; Brooks, III. C. Constant pH molecular dynamics using continuous titration coordinates. Proteins in press. 2004.
-
(2004)
Proteins
-
-
Lee, M.1
Salsbury Jr., F.2
Brooks III, C.3
-
50
-
-
20644449471
-
Modification of the generalized Born model suitable for macromolecules
-
Onufriev, A.; Bashford, D.; Case, D. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 2000, 104, 3712-3720.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.3
-
51
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer, M.; Karplus, M. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 1996, 100, 1578-1599.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
52
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
-
Schaefer, M.; Bartels, C.; Karplus, M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J. Mol. Biol. 1998, 284, 835-847.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 835-847
-
-
Schaefer, M.1
Bartels, C.2
Karplus, M.3
-
53
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and intl organic molecules
-
Cornell, W.; Cieplak, P.; Bayly, C.; Gould. I.; Merz, K.; Ferguson, D.; Spellmeyer, D.; Fox. T.; Caldwell, J.; Kollman, P. A second generation force field for the simulation of proteins, nucleic acids, and intl organic molecules. J. Am. Chem. Soc. 1995, 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, K.5
Ferguson, D.6
Spellmeyer, D.7
Fox, T.8
Caldwell, J.9
Kollman, P.10
-
54
-
-
0041784950
-
An all-atom empirical potential for molecular modelling and dynamics study of proteins
-
Mackerell, A.; Bashford, D.; Bellott, M.; Dunbrack, R.; Evanseck, J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.; Prodhom, B.; Reiher, W.; Roux, B.; Smith, J.; Stote, R.; Straub. J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. An all-atom empirical potential for molecular modelling and dynamics study of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph, 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, W.20
Roux, B.21
Smith, J.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiorkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
55
-
-
0141704114
-
A simple polarizable model of water based on classical Drude oscillators
-
Lamoureux, G.; MacKerell Jr.; A. D.; Roux, B. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 2003. 119, 5185-5197.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 5185-5197
-
-
Lamoureux, G.1
MacKerell Jr., A.D.2
Roux, B.3
-
56
-
-
0017100947
-
Theoretical studies of enzymic rcactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel. A.; Levitt, M. Theoretical studies of enzymic rcactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1976, 103, 227.
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227
-
-
Warshel, A.1
Levitt, M.2
-
57
-
-
0001084409
-
Quantum theory of solvation
-
Chandler, D. Quantum theory of solvation. J. Phys. Chem. 1984, 88, 3400-3407.
-
(1984)
J. Phys. Chem.
, vol.88
, pp. 3400-3407
-
-
Chandler, D.1
-
59
-
-
0007836334
-
Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton-transfer studies
-
Warshel, A. Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton-transfer studies. J. Phys. Chem. 1982, 86, 2218-2224.
-
(1982)
J. Phys. Chem.
, vol.86
, pp. 2218-2224
-
-
Warshel, A.1
-
60
-
-
33751143432
-
Free energy of ionic hydration
-
Hummer, G.; Pratt, L.; Garcia, A. Free energy of ionic hydration. J. Phys. Chem. 1996, 100, 1206-1215.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 1206-1215
-
-
Hummer, G.1
Pratt, L.2
Garcia, A.3
-
61
-
-
0037076338
-
Gaussian fluctuations and linear response in an electron-transfer protein
-
Simonson, T. Gaussian fluctuations and linear response in an electron-transfer protein. Proc. Natl. Acad. Sci. U.S.A 2002, 99, 6544-6549.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 6544-6549
-
-
Simonson, T.1
-
62
-
-
0025319619
-
Crystal structure of thioredoxin from Escherichia coli at 1.68 å resolution
-
Katti, S.; Lemaster, D.; Eklund, H. Crystal structure of thioredoxin from Escherichia coli at 1.68 å resolution. J. Mol. Biol. 1990, 212, 167.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 167
-
-
Katti, S.1
Lemaster, D.2
Eklund, H.3
-
63
-
-
0004268506
-
-
University of California, San Francisco
-
Case, D.; Pearlman, D.; Caldwell, J., III, T. C.; Ross, W.; Simmerling, C.; Darden, T.; Merz, K.; Stanton, R.; Cheng, A.; Vincent, J.; Crowley, M.; Tsui, V.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, J.; Massova, I.; Seibel, G.; Singh, U.; Weiner, P.; Kollman, P. AMBER 6; University of California, San Francisco, 1999.
-
(1999)
AMBER 6
-
-
Case, D.1
Pearlman, D.2
Caldwell III, T.C.J.3
Ross, W.4
Simmerling, C.5
Darden, T.6
Merz, K.7
Stanton, R.8
Cheng, A.9
Vincent, J.10
Crowley, M.11
Tsui, V.12
Radmer, R.13
Duan, Y.14
Pitera, J.15
Massova, I.16
Seibel, J.17
Massova, I.18
Seibel, G.19
Singh, U.20
Weiner, P.21
Kollman, P.22
more..
-
64
-
-
0004016501
-
Comparison of simple potential functions for stimulating liquid water
-
Jorgensen, W.; Chandrasekar, J.; Madura, J.; Impey, R.; Klein, M. Comparison of simple potential functions for stimulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekar, J.2
Madura, J.3
Impey, R.4
Klein, M.5
-
65
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.; Ciccotti, G.; Berendsen, H. Numerical integration of the Cartesian equations of motion for a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
66
-
-
84986512474
-
Charmm: A program for macromolecular energy, minimization, and molecular dynamics calculations
-
Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. Charmm: a program for macromolecular energy, minimization, and molecular dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
67
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics method
-
Nose, S. A unified formulation of the constant temperature molecular dynamics method. J. Chem. Phys. 1984, 81, 511-519.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nose, S.1
-
68
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 1985, 31, 1695-1697.
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.1
-
69
-
-
0035501755
-
Protein molecular dynamics with the Generalized Born/ACE solvent model
-
Calimet, N.; Schaefer, M.; Simonson, T. Protein molecular dynamics with the Generalized Born/ACE solvent model. Proteins 2001, 45, 144-158.
-
(2001)
Proteins
, vol.45
, pp. 144-158
-
-
Calimet, N.1
Schaefer, M.2
Simonson, T.3
-
70
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized Born model
-
in press
-
Onufriev, A.; Bashford, D.; Case, D. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins, 2004, in press.
-
(2004)
Proteins
-
-
Onufriev, A.1
Bashford, D.2
Case, D.3
-
71
-
-
0002636134
-
Pairwise descreening of solute charges from a dielectric medium
-
Hawkins, G.; Cramer, C.; Truhlar, D. Pairwise descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 1995, 246, 122-129.
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 122-129
-
-
Hawkins, G.1
Cramer, C.2
Truhlar, D.3
-
72
-
-
0037990993
-
-
Washington University School of Medicine
-
Ponder, J. Tinker: Washington University School of Medicine, 2000.
-
(2000)
Tinker
-
-
Ponder, J.1
-
73
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.; Postma, J.; van Gunsteren, W.; DiNola, A.; Haak, J. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 811, 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.811
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
DiNola, A.4
Haak, J.5
-
74
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling, C.; Strockbine, B.; Roitberg, A. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124, 11258-11259.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.3
-
75
-
-
0001087856
-
Calculation of free energy surfaces using the methods of thermodynamic perturbation theory
-
Tobias, D. J.; Brooks, C. L. Calculation of free energy surfaces using the methods of thermodynamic perturbation theory. Chem. Phys. Lett. 1987, 142, 472-476.
-
(1987)
Chem. Phys. Lett.
, vol.142
, pp. 472-476
-
-
Tobias, D.J.1
Brooks, C.L.2
-
76
-
-
0030774472
-
Multistate Gaussian model for electrostatic solvation free energies
-
Hummer, G.; Pratt, L.; Garcia, A. Multistate Gaussian model for electrostatic solvation free energies. J. Am. Chem. Soc. 1997, 119, 8523-8527.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 8523-8527
-
-
Hummer, G.1
Pratt, L.2
Garcia, A.3
-
77
-
-
5544264558
-
Gaussian fluctuation formula for electrostatic free energy changes
-
Levy, R.; Belhadj, M.; Kitchen, D. Gaussian fluctuation formula for electrostatic free energy changes. J. Chem. Phys. 1991, 95, 3627-3633.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 3627-3633
-
-
Levy, R.1
Belhadj, M.2
Kitchen, D.3
-
78
-
-
0001672288
-
Chemical and electro-chemical electron transfer theory
-
Marcus, R. Chemical and electro-chemical electron transfer theory. Annu. Rev. Phys. Chem. 1964, 15, 155-196.
-
(1964)
Annu. Rev. Phys. Chem.
, vol.15
, pp. 155-196
-
-
Marcus, R.1
-
79
-
-
0026012015
-
Microscopic theory of the dielectric properties of proteins
-
Simonson, T.; Perahia, D.; Brünger, A. T. Microscopic theory of the dielectric properties of proteins. Biophys. J. 1991, 59, 670-90.
-
(1991)
Biophys. J.
, vol.59
, pp. 670-690
-
-
Simonson, T.1
Perahia, D.2
Brünger, A.T.3
-
80
-
-
0030828226
-
Reorganization energy of cytochrome c revisited
-
Mucgge, I.; Qi, P.; Wand, A. J.; Chu, Z.; Warshel, A. Reorganization energy of cytochrome c revisited. J. Phys. Chem. B 1997. 101, 825-836.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 825-836
-
-
Mucgge, I.1
Qi, P.2
Wand, A.J.3
Chu, Z.4
Warshel, A.5
-
81
-
-
0000083584
-
Microscopic simulations of macroscopic dielectric constants of solvaled proteins
-
King, G.; Lee, F.; Warshel, A. Microscopic simulations of macroscopic dielectric constants of solvaled proteins. J. Chem. Phys. 1991, 95, 4366-4377.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 4366-4377
-
-
King, G.1
Lee, F.2
Warshel, A.3
-
82
-
-
0024365336
-
Hidden thermodynamics of mutant proteins: A molecular dynamics analysis
-
Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Hidden thermodynamics of mutant proteins: A molecular dynamics analysis. Science 1989, 244, 1069-1072.
-
(1989)
Science
, vol.244
, pp. 1069-1072
-
-
Gao, J.1
Kuczera, K.2
Tidor, B.3
Karplus, M.4
-
83
-
-
0032488817
-
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
-
Archontis, G.; Simonson, T.; Moras, D.; Karplus, M. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. J. Mol. Biol. 1998. 275. 823-846.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 823-846
-
-
Archontis, G.1
Simonson, T.2
Moras, D.3
Karplus, M.4
-
84
-
-
0042139644
-
Comparison of Generalized Born and Poisson models: Energetics and dynamics of HIV protease
-
David, L.; Luo, R.; Gilson, M. Comparison of Generalized Born and Poisson models: energetics and dynamics of HIV protease. J. Comput. Chem. 2000, 21, 295-309.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 295-309
-
-
David, L.1
Luo, R.2
Gilson, M.3
-
85
-
-
0037157693
-
Novel generalized Born methods
-
Lee, M.; Salsbury Jr., F.; Brooks, III, C. Novel generalized Born methods. J. Chem. Phys. 2002, 116, 10 606-10 614.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 10606-10614
-
-
Lee, M.1
Salsbury Jr., F.2
Brooks III, C.3
-
86
-
-
0035827113
-
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
-
Börjesson, U.; Hünenberger, P. H. Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines. J. Chem. Phys. 2001, 114, 9706-9719.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 9706-9719
-
-
Börjesson, U.1
Hünenberger, P.H.2
-
87
-
-
0030970305
-
Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration
-
Baptista, A.; Martel, P.; Petersen, S. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins 1997, 27, 523-544.
-
(1997)
Proteins
, vol.27
, pp. 523-544
-
-
Baptista, A.1
Martel, P.2
Petersen, S.3
-
88
-
-
0028925947
-
Evaluation of catalytic free energies in genetically modified proteins
-
Schweins, T.; Geyer, M.; Scheffzek, K.; Warshel, A.; Kalbitzer, H.; Wittinghofer, A. Evaluation of catalytic free energies in genetically modified proteins. Nat. Struct. Biol. 1995, 2, 36-44.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 36-44
-
-
Schweins, T.1
Geyer, M.2
Scheffzek, K.3
Warshel, A.4
Kalbitzer, H.5
Wittinghofer, A.6
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