-
1
-
-
84961981091
-
Implicit solvation models: Equilibria, structure, spectra, and dynamics
-
Cramer CJ, Truhlar DG. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem Rev 1999;9:2161-2200.
-
(1999)
Chem Rev
, vol.9
, pp. 2161-2200
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
2
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
3
-
-
0032319206
-
Calculation of proton binding thermodynamics in proteins
-
Beroza P, Case DA. Calculation of proton binding thermodynamics in proteins. Methods Enzymol 1998;295:170-189.
-
(1998)
Methods Enzymol
, vol.295
, pp. 170-189
-
-
Beroza, P.1
Case, D.A.2
-
4
-
-
85050521214
-
Biological applications of electrostatic calculations and Brownian dynamics
-
Madura JD, Davis ME, Gilson MK, Wade RC, Luty BA, McCammon JA. Biological applications of electrostatic calculations and Brownian dynamics. Rev Comp Chem 1994;5:229-267.
-
(1994)
Rev Comp Chem
, vol.5
, pp. 229-267
-
-
Madura, J.D.1
Davis, M.E.2
Gilson, M.K.3
Wade, R.C.4
Luty, B.A.5
McCammon, J.A.6
-
5
-
-
0029066848
-
Theory of electrostatic interactions in macromolecules
-
Gilson MK. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol 1995;5:216-223.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 216-223
-
-
Gilson, M.K.1
-
6
-
-
0031248940
-
Continuum electrostatic energies of macromolecules in aqueous solutions
-
Scarsi M, Apostolakis J, Caflisch A. Continuum electrostatic energies of macromolecules in aqueous solutions. J Phys Chem A 1997;101:8098-8106.
-
(1997)
J Phys Chem A
, vol.101
, pp. 8098-8106
-
-
Scarsi, M.1
Apostolakis, J.2
Caflisch, A.3
-
7
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comp Chem 2002;23:1244-1253.
-
(2002)
J Comp Chem
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
8
-
-
0012818236
-
Testing and comparison of empirical force fields: Techniques and problems
-
van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Leiden: ESCOM
-
Gelin BR. Testing and comparison of empirical force fields: techniques and problems. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer simulation of biomolecular sytems. Vol. 2. Leiden: ESCOM; 1993. p 127-146.
-
(1993)
Computer Simulation of Biomolecular Sytems
, vol.2
, pp. 127-146
-
-
Gelin, B.R.1
-
9
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Donini WWO, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Donini, W.W.O.10
Cieplak, P.11
Srinivasan, J.12
Case, D.A.13
Cheatham, T.E.14
-
10
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechnics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechnics 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.C.3
Hendrickson, T.4
-
11
-
-
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
-
12
-
-
0031075977
-
Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of Poisson-Boltzman equation
-
Edinger S, Cortis C, Shenkin P, Friesner R. Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of Poisson-Boltzman equation. J Phys Chem B 1997;101:1190-1197.
-
(1997)
J Phys Chem B
, vol.101
, pp. 1190-1197
-
-
Edinger, S.1
Cortis, C.2
Shenkin, P.3
Friesner, R.4
-
13
-
-
0000741414
-
A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
-
Jayaram B, Liu Y, Beveridge DJ. A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts. J Chem Phys 1998;109:1465-1470.
-
(1998)
J Chem Phys
, vol.109
, pp. 1465-1470
-
-
Jayaram, B.1
Liu, Y.2
Beveridge, D.J.3
-
14
-
-
0001246294
-
A generalized Born model based on a surface integral formulation
-
Aghosh A, Rapp CS, Friesner RA. A generalized Born model based on a surface integral formulation. J Phys Chem 1998;102:10983-10990.
-
(1998)
J Phys Chem
, vol.102
, pp. 10983-10990
-
-
Aghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
15
-
-
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
-
16
-
-
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
-
18
-
-
84961985307
-
Development of a Generalized Born model parametrization for proteins and nucleic acids
-
Dominy BN, Brooks CL. Development of a Generalized Born model parametrization for proteins and nucleic acids. J Phys Chem B 1999;103:3765-3773.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3765-3773
-
-
Dominy, B.N.1
Brooks, C.L.2
-
19
-
-
0042139644
-
Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease
-
David L, Luo R, Gilson MK. Comparison of generalized Born and Poisson models: energetics and dynamics of HIV protease. J Comp Chem 2000;21:295-309.
-
(2000)
J Comp Chem
, vol.21
, pp. 295-309
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
20
-
-
0037194983
-
Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models
-
Spassov VZ, Yan L, Szalma S. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J Phys Chem B 2002;106:8726-8738.
-
(2002)
J Phys Chem B
, vol.106
, pp. 8726-8738
-
-
Spassov, V.Z.1
Yan, L.2
Szalma, S.3
-
21
-
-
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
-
22
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids using a generalized Born solvation model
-
Tsui V, Case D. Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J Am Chem Soc 2000;122:2489-2498.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.2
-
23
-
-
0037230970
-
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
-
Wang T, Wade R. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003;50:158-169.
-
(2003)
Proteins
, vol.50
, pp. 158-169
-
-
Wang, T.1
Wade, R.2
-
24
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
-
Srinivasan J, Trevathan M, Beroza P, Case D. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor Chem Accts 1999;101:426-434.
-
(1999)
Theor Chem Accts
, vol.101
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.2
Beroza, P.3
Case, D.4
-
25
-
-
0037110472
-
Effective Born radii in the Generalized Born approximation: The importance of being perfect
-
Onufriev A, Case D, Bashford D. Effective Born radii in the Generalized Born approximation: the importance of being perfect. J Comp Chem 2002;23:1297-1304.
-
(2002)
J Comp Chem
, vol.23
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.2
Bashford, D.3
-
26
-
-
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, Still WC. The GB/SA continuum model for solvation: a fast analytical method for the calculation of approximate Born radii. J Phys Chem A 1997;101:3005-3014.
-
(1997)
J Phys Chem A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.2
Hollinger, F.3
Still, W.C.4
-
27
-
-
33748390341
-
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
-
Hawkins GD, Cramer CJ, Truhlar DG. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 1996;100:19824-19836.
-
(1996)
J Phys Chem
, vol.100
, pp. 19824-19836
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
28
-
-
0025661993
-
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
-
Schaefer M, Froemmel C. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J Mol Biol 1990;216:1045-1066.
-
(1990)
J Mol Biol
, vol.216
, pp. 1045-1066
-
-
Schaefer, M.1
Froemmel, C.2
-
29
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biochem Bioeng 1977;6:151-176.
-
(1977)
Annu Rev Biochem Bioeng
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
30
-
-
0346971105
-
Performance comparison of Generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of Generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comp Chem 2004;25:265-284.
-
(2004)
J Comp Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
31
-
-
0037225277
-
Structural details, pathways, and energetics of unfolding apomyoglobin
-
Onufriev A, Case DA, Bashford D. Structural details, pathways, and energetics of unfolding apomyoglobin. J Mol Biol 2003;325:555-567.
-
(2003)
J Mol Biol
, vol.325
, pp. 555-567
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
32
-
-
0031932824
-
Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding
-
Eliezer D, Yao J, Dyson HJ, Wright PE. Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding. Nat Struct Biol 1998;5:148-155.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 148-155
-
-
Eliezer, D.1
Yao, J.2
Dyson, H.J.3
Wright, P.E.4
-
33
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke H, Case DA. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comp Chem 2004;25:238-250.
-
(2004)
J Comp Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
34
-
-
14244273182
-
Theory and applications of the Generalized Born solvation model in macromolecular simulations
-
Tsui V, Case D. Theory and applications of the Generalized Born solvation model in macromolecular simulations. Biopolymers 2001;56:275-291.
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.2
-
35
-
-
0030745939
-
Accurate ab initio quantum chemical determinantion of the relative energies of peptide conformations and assessement of empirical force fields
-
Beachy MD, Chasman D, Murphy RB, Halgren TA, Friesner RA. Accurate ab initio quantum chemical determinantion of the relative energies of peptide conformations and assessement of empirical force fields. J Am Chem Soc 1997;119:5908-5920.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 5908-5920
-
-
Beachy, M.D.1
Chasman, D.2
Murphy, R.B.3
Halgren, T.A.4
Friesner, R.A.5
-
36
-
-
0035865992
-
Exploring the energy landscape of a β-hairpin in explicit solvent
-
Garcia AE, Sanbonmatsu KY. Exploring the energy landscape of a β-hairpin in explicit solvent. Proteins 2001;42:345-354.
-
(2001)
Proteins
, vol.42
, pp. 345-354
-
-
Garcia, A.E.1
Sanbonmatsu, K.Y.2
-
37
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg AE. 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.E.3
-
38
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over relaxation to solve the Poisson-Boltzmann equation
-
Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over relaxation to solve the Poisson-Boltzmann equation. J Comp Chem 1991;12:435-445.
-
(1991)
J Comp Chem
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
|