-
1
-
-
1642525904
-
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
-
M.A. Kastenholz, and P.H. Hünenberger Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods J Phys Chem B 108 2004 774 788 This article, which builds on previous work by Weber, Hünenberger and McCammon, describes some of the caveats of periodic simulations with insufficiently large simulation boxes.
-
(2004)
J Phys Chem B
, vol.108
, pp. 774-788
-
-
Kastenholz, M.A.1
Hünenberger, P.H.2
-
2
-
-
0032968133
-
Implicit solvent models
-
B. Roux, and T. Simonson Implicit solvent models Biophys Chem 78 1999 1 20
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
3
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
M. Feig, and C.L. Brooks Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr Opin Struct Biol 14 2004 217 224 This recent review of implicit solvent methods with a GB-specific focus is complementary to the current article.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 217-224
-
-
Feig, M.1
Brooks, C.L.2
-
4
-
-
34250928962
-
Volumen und hydratationswärme der ionen
-
M. Born Volumen und hydratationswärme der ionen Z Phys 1 1920 45 48 [Title translation: The volume and heat of hydration of ions]
-
(1920)
Z Phys
, vol.1
, pp. 45-48
-
-
Born, M.1
-
5
-
-
33947468892
-
Theory of protein titration curves. I. General equations for impenetrable spheres
-
C. Tanford, and J.G. Kirkwood Theory of protein titration curves. I. General equations for impenetrable spheres J Am Chem Soc 79 1957 5333 5339
-
(1957)
J Am Chem Soc
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.G.2
-
6
-
-
0035312551
-
Macromolecular electrostatics: Continuum models and their growing pains
-
T. Simonson Macromolecular electrostatics: continuum models and their growing pains Curr Opin Struct Biol 11 2001 243 252
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 243-252
-
-
Simonson, T.1
-
7
-
-
0035312897
-
Electrostatics calculations: Recent methodological advances and applications to membranes
-
D.J. Tobias Electrostatics calculations: recent methodological advances and applications to membranes Curr Opin Struct Biol 11 2001 253 261
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 253-261
-
-
Tobias, D.J.1
-
8
-
-
1642464809
-
Poisson-Boltzmann methods for biomolecular electrostatics
-
N.A. Baker Poisson-Boltzmann methods for biomolecular electrostatics Methods Enzymol 383 2004 94 118
-
(2004)
Methods Enzymol
, vol.383
, pp. 94-118
-
-
Baker, N.A.1
-
9
-
-
0036873086
-
The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology
-
F. Fogolari, A. Brigo, and H. Molinari The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology J Mol Recognit 15 2002 377 392
-
(2002)
J Mol Recognit
, vol.15
, pp. 377-392
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
10
-
-
0031234042
-
An integral equation to describe the solvation of polar molecules in liquid water
-
D. Beglov, and B. Roux An integral equation to describe the solvation of polar molecules in liquid water J Phys Chem B 101 1997 7821 7826
-
(1997)
J Phys Chem B
, vol.101
, pp. 7821-7826
-
-
Beglov, D.1
Roux, B.2
-
12
-
-
0000866128
-
Hydrophobic effect in protein folding and other noncovalent processes involving proteins
-
R.S. Spolar, J.H. Ha, and M.T. Record Jr. Hydrophobic effect in protein folding and other noncovalent processes involving proteins Proc Natl Acad Sci USA 86 1989 8382 8385
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 8382-8385
-
-
Spolar, R.S.1
Ha, J.H.2
Record Jr., M.T.3
-
13
-
-
0022596727
-
Solvation energy in protein folding and binding
-
D. Eisenberg, and A.D. McLachlan Solvation energy in protein folding and binding Nature 319 1986 199 203
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
14
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free energies using macroscopic solvent models J Phys Chem 98 1974 1978 1988
-
(1974)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
15
-
-
34250434907
-
Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory
-
F. Stillinger Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory J Sol Chem 2 1973 141 158
-
(1973)
J Sol Chem
, vol.2
, pp. 141-158
-
-
Stillinger, F.1
-
16
-
-
0035281357
-
Computer simulation of protein-protein interactions
-
A.H. Elcock, D. Sept, and J.A. McCammon Computer simulation of protein-protein interactions J Phys Chem B 105 2001 1504 1518
-
(2001)
J Phys Chem B
, vol.105
, pp. 1504-1518
-
-
Elcock, A.H.1
Sept, D.2
McCammon, J.A.3
-
17
-
-
4444323489
-
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
-
J. Wagoner, and N.A. Baker Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models J Comput Chem 25 2004 1623 1629 This paper compares PB/SA calculations with explicit solvent simulations. The authors observe strong correlation between implicit and explicit solvent polar forces, but poor agreement for apolar forces.
-
(2004)
J Comput Chem
, vol.25
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.A.2
-
18
-
-
1442330396
-
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
-
E. Gallichio, and R.M. Levy AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling J Comput Chem 25 2004 479 499 A very promising formulation of the GB approach, together with a novel description of apolar energetics. It shows sensitivity to both large and small conformational changes, which makes it a promising method for a variety of molecular simulations.
-
(2004)
J Comput Chem
, vol.25
, pp. 479-499
-
-
Gallichio, E.1
Levy, R.M.2
-
19
-
-
0347787914
-
Continuum solvent modeling of nonpolar solvation: Improvement by separating surface area dependent cavity and dispersion contributions
-
M. Zacharias Continuum solvent modeling of nonpolar solvation: improvement by separating surface area dependent cavity and dispersion contributions J Phys Chem A 107 2003 3000 3004 This article discusses the importance of including dispersion (van der Waals) interactions in addition to cavity-related SA terms. The author develops a new apolar hydration model based on this argument and shows that it generates much better agreement with explicit solvent simulations.
-
(2003)
J Phys Chem a
, vol.107
, pp. 3000-3004
-
-
Zacharias, M.1
-
20
-
-
0034823225
-
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers
-
J.W. Pitera, and W.F. van Gunsteren The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers J Am Chem Soc 123 2001 3163 3164
-
(2001)
J Am Chem Soc
, vol.123
, pp. 3163-3164
-
-
Pitera, J.W.1
Van Gunsteren, W.F.2
-
21
-
-
0141565502
-
A simple analytical model of water
-
T.M. Truskett, and K.A. Dill A simple analytical model of water Biophys Chem 105 2003 449 459 A discussion of the properties of the two-dimensional 'Mercedes-Benz' model of water and its qualitative agreement with experimental observations.
-
(2003)
Biophys Chem
, vol.105
, pp. 449-459
-
-
Truskett, T.M.1
Dill, K.A.2
-
23
-
-
0037899660
-
Polarizable atomic multipole water model for molecular mechanics simulation
-
P. Ren, and J.W. Ponder Polarizable atomic multipole water model for molecular mechanics simulation J Phys Chem B 107 2003 5933 5947 A description of a polarizable explicit water model (AMOEBA) that provides remarkable agreement with a variety of experimental parameters (see also several follow-up papers published on the properties of this water model and corresponding solute force field parameters). These are the simulation results that implicit solvent models should aspire to achieve.
-
(2003)
J Phys Chem B
, vol.107
, pp. 5933-5947
-
-
Ren, P.1
Ponder, J.W.2
-
24
-
-
0034831674
-
Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model
-
S.W. Rick Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model J Chem Phys 114 2001 2276 2283
-
(2001)
J Chem Phys
, vol.114
, pp. 2276-2283
-
-
Rick, S.W.1
-
25
-
-
0035424605
-
Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function
-
H.A. Stern, F. Rittner, B.J. Berne, and R.A. Friesner Combined fluctuating charge and polarizable dipole models: application to a five-site water potential function J Chem Phys 115 2001 2237 2251
-
(2001)
J Chem Phys
, vol.115
, pp. 2237-2251
-
-
Stern, H.A.1
Rittner, F.2
Berne, B.J.3
Friesner, R.A.4
-
26
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: The importance of being perfect
-
A. Onufriev, D.A. Case, and D. Bashford Effective Born radii in the generalized Born approximation: the importance of being perfect J Comput Chem 23 2002 1297 1304
-
(2002)
J Comput Chem
, vol.23
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
27
-
-
2942700087
-
Comment on "can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?" the Poisson-Boltzmann equation
-
R. Zhou, G. Krilov, and B.J. Berne Comment on "can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?" The Poisson-Boltzmann equation J Phys Chem B 108 2004 7528 7530
-
(2004)
J Phys Chem B
, vol.108
, pp. 7528-7530
-
-
Zhou, R.1
Krilov, G.2
Berne, B.J.3
-
28
-
-
0346971105
-
Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks III Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J Comput Chem 25 2004 265 284 A side-by-side comparison of the accuracy and efficiency of several GB and PB implementations. Although one can argue about the usefulness of the efficiency benchmarks (particularly as our code was rated as relatively slower than others), this paper is a very useful guide to the 'state of the art' in GB and PB methods.
-
(2004)
J Comput Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
-
29
-
-
0032968444
-
Optimized atomic radii for protein continuum electrostatics solvation forces
-
M. Nina, W. Im, and B. Roux Optimized atomic radii for protein continuum electrostatics solvation forces Biophys Chem 78 1999 89 96
-
(1999)
Biophys Chem
, vol.78
, pp. 89-96
-
-
Nina, M.1
Im, W.2
Roux, B.3
-
30
-
-
8844228899
-
Not ions alone: Barriers to ion permeation in nanopores and channels
-
O. Beckstein, K. Tai, and M.S.P. Sansom Not ions alone: barriers to ion permeation in nanopores and channels J Am Chem Soc 126 2004 14694 14695 This short article describes the inability of implicit solvent models to correctly describe the energetic barrier to ion passage through a hydrophobic membrane pore.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 14694-14695
-
-
Beckstein, O.1
Tai, K.2
Sansom, M.S.P.3
-
31
-
-
0037234043
-
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
-
H. Gouda, I.D. Kuntz, D.A. Case, and P.A. Kollman Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods Biopolymers 68 2003 16 34 The authors used the MM (molecular mechanics)/PBSA method to study ligand binding to RNA. They demonstrate that the implicit solvent method doesn't perform as well as the explicit solvent technique, presumably due to important interactions mediated by discrete water in the first hydration shell.
-
(2003)
Biopolymers
, vol.68
, pp. 16-34
-
-
Gouda, H.1
Kuntz, I.D.2
Case, D.A.3
Kollman, P.A.4
-
32
-
-
0036708447
-
Bridging the implicit and explicit solvent approaches for membrane electrostatics
-
J.-H. Lin, N.A. Baker, and J.A. McCammon Bridging the implicit and explicit solvent approaches for membrane electrostatics Biophys J 83 2002 1374 1379
-
(2002)
Biophys J
, vol.83
, pp. 1374-1379
-
-
Lin, J.-H.1
Baker, N.A.2
McCammon, J.A.3
-
33
-
-
7044249333
-
Grand canonical Monte Carlo simulations of water in protein environments
-
H.-J. Woo, A.R. Dinner, and B. Roux Grand canonical Monte Carlo simulations of water in protein environments J Chem Phys 121 2004 6392 6400
-
(2004)
J Chem Phys
, vol.121
, pp. 6392-6400
-
-
Woo, H.-J.1
Dinner, A.R.2
Roux, B.3
-
34
-
-
3142704441
-
A simple correlation-corrected Poisson-Boltzmann theory
-
J. Forsman A simple correlation-corrected Poisson-Boltzmann theory J Phys Chem B 108 2004 9236 9245
-
(2004)
J Phys Chem B
, vol.108
, pp. 9236-9245
-
-
Forsman, J.1
-
35
-
-
0041306048
-
Like-charge attraction between polyelectrolytes induced by counterion charge density waves
-
T.E. Angelini, H. Liang, W. Wriggers, and G.C.L. Wong Like-charge attraction between polyelectrolytes induced by counterion charge density waves Proc Natl Acad Sci USA 100 2003 8634 8637 This experimental paper demonstrates an ionic phenomenon that cannot be reproduced by mean field implicit solvent models such as PB theory.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 8634-8637
-
-
Angelini, T.E.1
Liang, H.2
Wriggers, W.3
Wong, G.C.L.4
-
36
-
-
2442437667
-
Attraction of like-charged macro-ions in the strong-coupling limit
-
A. Naji, and R.R. Netz Attraction of like-charged macro-ions in the strong-coupling limit Eur Phys J E 13 2004 43 59
-
(2004)
Eur Phys J e
, vol.13
, pp. 43-59
-
-
Naji, A.1
Netz, R.R.2
-
37
-
-
0036389892
-
Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory
-
W. Im, and B. Roux Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory J Mol Biol 322 2002 851 869
-
(2002)
J Mol Biol
, vol.322
, pp. 851-869
-
-
Im, W.1
Roux, B.2
-
38
-
-
0042845840
-
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
-
E.J. Sorin, Y.M. Rhee, B.J. Nakatani, and V.S. Pande Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations Biophys J 85 2003 790 803 This article describes stochastic simulations together with GB/SA solutions to simulate nucleic acid hairpin formation. An interesting aspect of this simulation is the lack of explicit ions. The authors discuss this omission, together with some comments on the state of GB simulations.
-
(2003)
Biophys J
, vol.85
, pp. 790-803
-
-
Sorin, E.J.1
Rhee, Y.M.2
Nakatani, B.J.3
Pande, V.S.4
-
39
-
-
0141453063
-
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
-
T. Grycuk Deficiency of the Coulomb-field approximation in the generalized Born model: an improved formula for Born radii evaluation J Chem Phys 119 2003 4817 4826
-
(2003)
J Chem Phys
, vol.119
, pp. 4817-4826
-
-
Grycuk, T.1
-
40
-
-
7544239151
-
An assessment of potential of mean force calculations with implicit solvent models
-
C.M. Stultz An assessment of potential of mean force calculations with implicit solvent models J Phys Chem B 108 2004 16525 16532 A comparison of various implicit solvent models (not PB) with explicit solvent simulations and experimental data. The explicit solvent simulations give good agreement with experiment, whereas the implicit solvent simulations perform badly.
-
(2004)
J Phys Chem B
, vol.108
, pp. 16525-16532
-
-
Stultz, C.M.1
-
41
-
-
0037230970
-
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
-
T. Wang, and R.C. Wade Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation Proteins 50 2003 158 169 An interesting comparison of simple implicit solvent methods, including GB methods, distance-dependent dielectric approaches and an SA model.
-
(2003)
Proteins
, vol.50
, pp. 158-169
-
-
Wang, T.1
Wade, R.C.2
-
42
-
-
7044260905
-
Free energies of hydration from a generalized Born model and an all-atom force field
-
W.L. Jorgensen, J.P. Ulmschneider, and J. Tirado-Rives Free energies of hydration from a generalized Born model and an all-atom force field J Phys Chem B 108 2004 16264 16270 This paper details the strong agreement between GB/SA models and experimental results for the solvation energies of small organic molecules.
-
(2004)
J Phys Chem B
, vol.108
, pp. 16264-16270
-
-
Jorgensen, W.L.1
Ulmschneider, J.P.2
Tirado-Rives, J.3
-
43
-
-
2942597884
-
First-shell solvation of ion pairs: Correction of systematic errors in implicit solvent models
-
Z. Yu, M.P. Jacobson, J. Josovitz, C.S. Rapp, and R.A. Friesner First-shell solvation of ion pairs: correction of systematic errors in implicit solvent models J Phys Chem B 108 2004 6643 6654 This article addresses several problems with PB and GB models in the context of ionic interactions. Like other articles in this area, it notes that implicit solvent models incorrectly described interactions between charged groups, apparently due to incorrect treatment of first-shell solvation. However, the authors then proceed to demonstrate that these errors can be corrected through a hybrid method in which the offending waters are modeled explicitly.
-
(2004)
J Phys Chem B
, vol.108
, pp. 6643-6654
-
-
Yu, Z.1
Jacobson, M.P.2
Josovitz, J.3
Rapp, C.S.4
Friesner, R.A.5
-
44
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
H. Gohlke, and D.A. Case Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf J Comput Chem 25 2004 238 250
-
(2004)
J Comput Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
45
-
-
11144284604
-
ISIM: A program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules
-
A. Vitalis, N.A. Baker, and J.A. McCammon ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules Mol Simul 30 2004 45 61
-
(2004)
Mol Simul
, vol.30
, pp. 45-61
-
-
Vitalis, A.1
Baker, N.A.2
McCammon, J.A.3
-
46
-
-
1242287118
-
Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution
-
B. Egwolf, and P. Tavan Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution J Chem Phys 120 2004 2056 2068 The extension of a novel approach to approximating the solution to Poisson or PB equations using atom-centered inducible dipoles.
-
(2004)
J Chem Phys
, vol.120
, pp. 2056-2068
-
-
Egwolf, B.1
Tavan, P.2
-
47
-
-
0020475509
-
Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
-
J. Warwicker, and H.C. Watson Calculation of the electric potential in the active site cleft due to alpha-helix dipoles J Mol Biol 157 1982 671 679
-
(1982)
J Mol Biol
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
48
-
-
9244259076
-
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
-
N.V. Prabhu, P. Zhu, and K.A. Sharp Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method J Comput Chem 25 2004 2049 2064 A demonstration of the efficiency and accuracy (in terms of molecular dynamics stability) of the ZAP PB solver.
-
(2004)
J Comput Chem
, vol.25
, pp. 2049-2064
-
-
Prabhu, N.V.1
Zhu, P.2
Sharp, K.A.3
-
49
-
-
0347410858
-
A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
-
••] in their comparison of PB solvers, the authors report that this implementation is also very fast and comparable in efficiency to GB.
-
(2003)
J Chem Phys
, vol.119
, pp. 11035-11047
-
-
Lu, Q.1
Luo, R.2
-
50
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
R. Luo, L. David, and M.K. Gilson Accelerated Poisson-Boltzmann calculations for static and dynamic systems J Comput Chem 23 2002 1244 1253
-
(2002)
J Comput Chem
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
51
-
-
0037103014
-
Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation
-
B.Z. Lu, W.Z. Chen, C.X. Wang, and X.J. Xu Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation Proteins 48 2002 497 504
-
(2002)
Proteins
, vol.48
, pp. 497-504
-
-
Lu, B.Z.1
Chen, W.Z.2
Wang, C.X.3
Xu, X.J.4
-
52
-
-
0038650794
-
Protocol for MM/PBSA molecular dynamics simulations of proteins
-
F. Fogolari, A. Brigo, and H. Molinari Protocol for MM/PBSA molecular dynamics simulations of proteins Biophys J 85 2003 159 166 A very readable introduction to PB methods, together with some modifications to accelerate solution of the PB equation in a molecular dynamics setting.
-
(2003)
Biophys J
, vol.85
, pp. 159-166
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
53
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, and W. Wang Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc Chem Res 33 2000 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
Wang, W.10
-
54
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
J.M.J. Swanson, R.H. Henchman, and J.A. McCammon Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy Biophys J 86 2004 67 74 An analysis of MM/PBSA in the context of statistical mechanics, together with a discussion of the application of the theory to molecular dynamics simulations.
-
(2004)
Biophys J
, vol.86
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
55
-
-
0037305552
-
On the evaluation and optimization of protein X-ray structures for pKa calculations
-
as of titratable residues in proteins. Interestingly, unlike the work of Georgescu et al. [56], Nielsen and McCammon find that the inclusion of flexibility does not improve the accuracy of the calculations.
-
(2003)
Protein Sci
, vol.12
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
56
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins
-
R.E. Georgescu, E.G. Alexov, and M.R. Gunner Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins Biophys J 83 2002 1731 1748
-
(2002)
Biophys J
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
57
-
-
4644264472
-
Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme
-
J. Warwicker Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme Protein Sci 13 2004 2793 2805
-
(2004)
Protein Sci
, vol.13
, pp. 2793-2805
-
-
Warwicker, J.1
-
58
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
A. Nicholls, and B. Honig A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J Comput Chem 12 1991 435 445
-
(1991)
J Comput Chem
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
59
-
-
84988141840
-
Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods
-
M.E. Davis, and J.A. McCammon Solving the finite difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods J Comput Chem 10 1989 386 391
-
(1989)
J Comput Chem
, vol.10
, pp. 386-391
-
-
Davis, M.E.1
McCammon, J.A.2
-
60
-
-
0000525721
-
Multigrid solution of the Poisson-Boltzmann equation
-
M. Holst, and F. Saied Multigrid solution of the Poisson-Boltzmann equation J Comput Chem 14 1993 105 113
-
(1993)
J Comput Chem
, vol.14
, pp. 105-113
-
-
Holst, M.1
Saied, F.2
-
61
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc Natl Acad Sci USA 98 2001 10037 10041
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
62
-
-
0035327566
-
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
-
N.A. Baker, D. Sept, M.J. Holst, and J.A. McCammon The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers IBM Journal of Research and Development 45 2001 427 438
-
(2001)
IBM Journal of Research and Development
, vol.45
, pp. 427-438
-
-
Baker, N.A.1
Sept, D.2
Holst, M.J.3
McCammon, J.A.4
-
63
-
-
0037142983
-
A finite difference domain decomposition method using local corrections for the solution of Poisson's equation
-
G.T. Balls, and P. Colella A finite difference domain decomposition method using local corrections for the solution of Poisson's equation J Comput Phys 180 2002 25 53
-
(2002)
J Comput Phys
, vol.180
, pp. 25-53
-
-
Balls, G.T.1
Colella, P.2
-
64
-
-
0142246157
-
The Poisson-Boltzmann equation
-
K.B. Lipkowitz R. Larter T.R. Cundari John Wiley and Sons, Inc
-
G. Lamm The Poisson-Boltzmann equation K.B. Lipkowitz R. Larter T.R. Cundari Reviews in Computational Chemistry vol 19 2003 John Wiley and Sons, Inc 147 366
-
(2003)
Reviews in Computational Chemistry
, vol.19
, pp. 147-366
-
-
Lamm, G.1
-
65
-
-
2342454337
-
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
-
A.H. Boschitsch, and M.O. Fenley Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation J Comput Chem 25 2004 935 955
-
(2004)
J Comput Chem
, vol.25
, pp. 935-955
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
66
-
-
0037328258
-
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
-
A.J. Bordner, and G.A. Huber Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution J Comput Chem 24 2003 353 367
-
(2003)
J Comput Chem
, vol.24
, pp. 353-367
-
-
Bordner, A.J.1
Huber, G.A.2
-
67
-
-
0001439211
-
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
-
C.M. Cortis, and R.A. Friesner Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes J Comput Chem 18 1997 1591 1608
-
(1997)
J Comput Chem
, vol.18
, pp. 1591-1608
-
-
Cortis, C.M.1
Friesner, R.A.2
-
68
-
-
0000486193
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
-
M. Holst, N. Baker, and F. Wang Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples J Comput Chem 21 2000 1319 1342
-
(2000)
J Comput Chem
, vol.21
, pp. 1319-1342
-
-
Holst, M.1
Baker, N.2
Wang, F.3
-
69
-
-
0000486194
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
-
N. Baker, M. Holst, and F. Wang Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems J Comput Chem 21 2000 1343 1352
-
(2000)
J Comput Chem
, vol.21
, pp. 1343-1352
-
-
Baker, N.1
Holst, M.2
Wang, F.3
-
70
-
-
0023280069
-
Calculation of electrostatic potentials in an enzyme active site
-
M.K. Gilson, and B.H. Honig Calculation of electrostatic potentials in an enzyme active site Nature 330 1987 84 86
-
(1987)
Nature
, vol.330
, pp. 84-86
-
-
Gilson, M.K.1
Honig, B.H.2
-
71
-
-
0035971738
-
A smooth permittivity function for Poisson-Boltzmann solvation methods
-
J.A. Grant, B.T. Pickup, and A. Nicholls A smooth permittivity function for Poisson-Boltzmann solvation methods J Comput Chem 22 2001 608 640
-
(2001)
J Comput Chem
, vol.22
, pp. 608-640
-
-
Grant, J.A.1
Pickup, B.T.2
Nicholls, A.3
-
72
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
-
W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects J Comput Chem 23 2002 128 137
-
(2002)
J Comput Chem
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
73
-
-
85033849708
-
Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy
-
Z. Zhou, P. Payne, M. Vasquez, N. Kuhn, and M. Levitt Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy J Comput Chem 17 1996 1344 1351
-
(1996)
J Comput Chem
, vol.17
, pp. 1344-1351
-
-
Zhou, Z.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
-
74
-
-
84986532558
-
Electrostatic energy calculations by a finite-difference method: Rapid calculation of charge-solvent interaction energies
-
B. Luty, M. Davis, and J.A. McCammon Electrostatic energy calculations by a finite-difference method: rapid calculation of charge-solvent interaction energies J Comput Chem 13 1992 768 771
-
(1992)
J Comput Chem
, vol.13
, pp. 768-771
-
-
Luty, B.1
Davis, M.2
McCammon, J.A.3
-
76
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J Mol Biol 55 1971 379 400
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
77
-
-
0027159949
-
The molecular surface package
-
M.L. Connolly The molecular surface package J Mol Graph 11 1993 139 141
-
(1993)
J Mol Graph
, vol.11
, pp. 139-141
-
-
Connolly, M.L.1
-
78
-
-
0032096837
-
Continuum solvation model: Electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
-
W. Im, D. Beglov, and B. Roux Continuum solvation model: electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput Phys Commun 111 1998 59 75
-
(1998)
Comput Phys Commun
, vol.111
, pp. 59-75
-
-
Im, W.1
Beglov, D.2
Roux, B.3
-
79
-
-
0038650855
-
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
-
F. Dong, M. Vijaykumar, and H.X. Zhou Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar Biophys J 85 2003 49 60 This paper reveals one of PB theory's 'dirty little secrets': one can obtain very different results using different discontinuous dielectric functions (e.g. van der Waals versus Connolly surfaces). Furthermore, the choice of SA apolar coefficient also depends on the surface definition. This isn't terribly surprising or troubling, considering the shift to continuous dielectric functions in the PB community; however, it is a good fact to keep in mind when running or analyzing PB calculations.
-
(2003)
Biophys J
, vol.85
, pp. 49-60
-
-
Dong, F.1
Vijaykumar, M.2
Zhou, H.X.3
-
80
-
-
0037109541
-
Electrostatic free energy calculations using the generalized solvent boundary potential method
-
N.K. Banavali, W. Im, and B. Roux Electrostatic free energy calculations using the generalized solvent boundary potential method J Chem Phys 117 2002 7381 7388
-
(2002)
J Chem Phys
, vol.117
, pp. 7381-7388
-
-
Banavali, N.K.1
Im, W.2
Roux, B.3
-
81
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Y.N. Vorobjev, and J. Hermans ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model Biophys Chem 78 1999 195 205
-
(1999)
Biophys Chem
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
82
-
-
9244224092
-
An efficient hybrid explicit/implicit solvent method for biomolecular simulations
-
M.S. Lee, F.R. Salsbury Jr., and M.A. Olson An efficient hybrid explicit/implicit solvent method for biomolecular simulations J Comput Chem 25 2004 1967 1978
-
(2004)
J Comput Chem
, vol.25
, pp. 1967-1978
-
-
Lee, M.S.1
Salsbury Jr., F.R.2
Olson, M.A.3
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