-
2
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization and dynamics calculations
-
10.1002/jcc.540040211 0192-8651
-
Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S and Karplus M 1983 CHARMM: a program for macromolecular energy, minimization and dynamics calculations J. Comput. Chem. 4 187-217
-
(1983)
J. Comput. Chem.
, vol.4
, Issue.2
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
3
-
-
0021476470
-
Calculations of electrostatic interactions in biological systems and in solutions
-
10.1017/S0033583500005333 0033-5835
-
Warshel A and Russell S T 1984 Calculations of electrostatic interactions in biological systems and in solutions Q. Rev. Biophys. 17 283-422
-
(1984)
Q. Rev. Biophys.
, vol.17
, Issue.3
, pp. 283-422
-
-
Warshel, A.1
Russell, S.T.2
-
4
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
10.1021/cr00101a005 0009-2665
-
Davis M E and McCammon J A 1990 Electrostatics in biomolecular structure and dynamics Chem. Rev. 90 509-21
-
(1990)
Chem. Rev.
, vol.90
, Issue.3
, pp. 509-521
-
-
Davis, M.E.1
McCammon, J.A.2
-
6
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical applications
-
10.1021/j100108a002 0022-3654
-
Honig B, Sharp K and Yang A S 1993 Macroscopic models of aqueous solutions: biological and chemical applications J. Phys. Chem. 97 1101-9
-
(1993)
J. Phys. Chem.
, vol.97
, Issue.6
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.S.3
-
7
-
-
11744256643
-
Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
-
Tomasi J and Persico M 1994 Molecular interactions in solution: an overview of methods based on continuous descriptions of the solvent Chem. Rev. 94 2027-94 (Pubitemid 124000195)
-
(1994)
Chemical Reviews
, vol.94
, Issue.7
, pp. 2027-2094
-
-
Tomasi, J.1
Persico, M.2
-
8
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
10.1126/science.7761829 0036-8075
-
Honig B and Nicholls A 1995 Classical electrostatics in biology and chemistry Science 268 1144-9
-
(1995)
Science
, vol.268
, Issue.5214
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
9
-
-
84961981091
-
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
-
Cramer C J and Truhlar D G 1999 Implicit solvation models: equilibria, structure, spectra and dynamics Chem. Rev. 99 2161-200 (Pubitemid 129585183)
-
(1999)
Chemical Reviews
, vol.99
, Issue.8
, pp. 2161-2200
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
10
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
DOI 10.1021/cr990052a
-
Orozco M and Luque F J 2000 Theoretical methods for the description of the solvent effect in biomolecular systems Chem. Rev. 100 4187-225 (Pubitemid 32067769)
-
(2000)
Chemical Reviews
, vol.100
, Issue.11
, pp. 4187-4225
-
-
Orozco, M.1
Luque, F.J.2
-
11
-
-
0035312551
-
Macromolecular electrostatics: Continuum models and their growing pains
-
DOI 10.1016/S0959-440X(00)00197-4
-
Simonson T 2001 Macromolecular electrostatics: continuum models and their growing pains Curr. Opin. Struct. Biol. 11 243-52 (Pubitemid 32289429)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.2
, pp. 243-252
-
-
Simonson, T.1
-
12
-
-
0037529067
-
Electrostatics and dynamics of proteins
-
DOI 10.1088/0034-4885/66/5/202
-
Simonson T 2003 Electrostatics and dynamics of proteins Rep. Prog. Phys. 66 737-87 (Pubitemid 36685137)
-
(2003)
Reports on Progress in Physics
, vol.66
, Issue.5
, pp. 737-787
-
-
Simonson, T.1
-
13
-
-
0035312897
-
Electrostatics calculations: Recent methodological advances and applications to membranes
-
DOI 10.1016/S0959-440X(00)00198-6
-
Tobias D J 2001 Electrostatics calculations: recent methodological advances and applications to membranes Curr. Opin. Struct. Biol. 11 253-61 (Pubitemid 32289430)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.2
, pp. 253-261
-
-
Tobias, D.J.1
-
14
-
-
1642464809
-
Poisson-Boltzmann Methods for Biomolecular Electrostatics
-
DOI 10.1016/S0076-6879(04)83005-2
-
Baker N A 2004 Poisson-Boltzmann methods for biomolecular electrostatics Methods Enzymol. 383 94 (Pubitemid 38401788)
-
(2004)
Methods in Enzymology
, vol.383
, pp. 94-118
-
-
Baker, N.A.1
-
15
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
DOI 10.1016/j.sbi.2004.03.009, PII S0959440X04000430
-
Feig M and Brooks C L III 2004 Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr. Opin. Struct. Biol. 14 217-24 (Pubitemid 38495800)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.2
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
16
-
-
17044392602
-
Improving implicit solvent simulations: A Poisson-centric view
-
10.1016/j.sbi.2005.02.001 0959-440X
-
Baker N A 2005 Improving implicit solvent simulations: a Poisson-centric view Curr. Opin. Struct. Biol. 15 137-43
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, Issue.2
, pp. 137-143
-
-
Baker, N.A.1
-
17
-
-
33750053883
-
Biomolecular applications of Poisson-Boltzmann methods
-
Baker N A 2005 Biomolecular applications of Poisson-Boltzmann methods Rev. Comput. Chem. 21 349-79 (Pubitemid 44578721)
-
(2005)
Reviews in Computational Chemistry
, vol.21
, pp. 349-379
-
-
Baker, N.A.1
-
18
-
-
84961980477
-
Quantum mechanical continuum solvation models
-
DOI 10.1021/cr9904009
-
Tomasi J, Mennucci B and Cammi R 2005 Quantum mechanical continuum solvation models Chem. Rev. 105 2999-3093 (Pubitemid 41222791)
-
(2005)
Chemical Reviews
, vol.105
, Issue.8
, pp. 2999-3093
-
-
Tomasi, J.1
Mennucci, B.2
Cammi, R.3
-
19
-
-
33748273567
-
Extending the horizon: Towards the efficient modeling of large biomolecular complexes in atomic detail
-
DOI 10.1007/s00214-005-0062-4
-
Feig M, Chocholoušová J and Tanizaki S 2006 Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail Theor. Chem. Acc. 116 194-205 (Pubitemid 44318424)
-
(2006)
Theoretical Chemistry Accounts
, vol.116
, Issue.1-3
, pp. 194-205
-
-
Feig, M.1
Chocholousova, J.2
Tanizaki, S.3
-
20
-
-
33846076119
-
Modeling electrostatic effects in proteins
-
DOI 10.1016/j.bbapap.2006.08.007, PII S1570963906002809
-
Warshel A, Sharma P K, Kato M and Parson M W 2006 Modeling electrostatic effects in proteins Biochimica Biophys. Acta 1764 1647-76 (Pubitemid 46070172)
-
(2006)
Biochimica et Biophysica Acta - Proteins and Proteomics
, vol.1764
, Issue.11
, pp. 1647-1676
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Parson, W.W.4
-
21
-
-
44849122543
-
Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications
-
1815-2406
-
Lu B, Zhou Y C, Holst M J and McCammon J A 2008 Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications Commun. Comput. Phys. 3 973-1009 (available at http://www.global-sci.com/issue/ contents/3/issue5.html)
-
(2008)
Commun. Comput. Phys.
, vol.3
, pp. 973-1009
-
-
Lu, B.1
Zhou, Y.C.2
Holst, M.J.3
McCammon, J.A.4
-
22
-
-
0033654297
-
Generalized Born models of macromolecular solvation effects
-
10.1146/annurev.physchem.51.1.129 0066-426X
-
Bashford D and Case D A 2000 Generalized Born models of macromolecular solvation effects Annu. Rev. Phys. Chem. 51 129-52
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, Issue.1
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
23
-
-
84863070592
-
Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
-
10.1137/090774288 0036-1445
-
Xu Z and Cai W 2011 Fast analytical methods for macroscopic electrostatic models in biomolecular simulations SIAM Rev. 53 683-720
-
(2011)
SIAM Rev.
, vol.53
, Issue.4
, pp. 683-720
-
-
Xu, Z.1
Cai, W.2
-
24
-
-
84986522972
-
Dielectric boundary smoothing in finite difference solutions of the Poisson equation: An approach to improve accuracy and convergence
-
10.1002/jcc.540120718 0192-8651
-
Davis M E and McCammon J A 1991 Dielectric boundary smoothing in finite difference solutions of the Poisson equation: an approach to improve accuracy and convergence J. Comput. Chem. 12 909-12
-
(1991)
J. Comput. Chem.
, vol.12
, Issue.7
, pp. 909-912
-
-
Davis, M.E.1
McCammon, J.A.2
-
25
-
-
0035971738
-
A smooth permittivity function for Poisson-Boltzmann solvation methods
-
DOI 10.1002/jcc.1032
-
Grant J A, Pickup B T and Nicholls A 2001 A smooth permittivity function for Poisson-Boltzmann solvation methods J. Comput. Chem. 22 608-40 (Pubitemid 32382607)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.6
, pp. 608-640
-
-
Grant, J.A.1
-
26
-
-
20644431615
-
Theory of solutions of molecules containing widely separated charges with special application to zwitterions
-
10.1063/1.1749489 0021-9606
-
Kirkwood J G 1934 Theory of solutions of molecules containing widely separated charges with special application to zwitterions J. Chem. Phys. 2 351
-
(1934)
J. Chem. Phys.
, vol.2
, Issue.7
, pp. 351
-
-
Kirkwood, J.G.1
-
27
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: The importance of being perfect
-
DOI 10.1002/jcc.10126
-
Onufriev A, Case D A and Bashford D 2002 Effective Born radii in the generalized Born approximation: the importance of being perfect J. Comput. Chem. 23 1297-304 (Pubitemid 35186231)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.14
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
28
-
-
0000396658
-
A fast algorithm for particle simulations
-
10.1016/0021-9991(87)90140-9 0021-9991
-
Greengard L and Rokhlin V 1987 A fast algorithm for particle simulations J. Comput. Phys. 73 325-48
-
(1987)
J. Comput. Phys.
, vol.73
, Issue.2
, pp. 325-348
-
-
Greengard, L.1
Rokhlin, V.2
-
30
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kale L and Schulten K 2005 Scalable molecular dynamics with NAMD J. Comput. Chem. 26 1781-802 (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
31
-
-
0000525721
-
Multigrid solution of the Poisson-Boltzmann equation
-
10.1002/jcc.540140114 0192-8651
-
Holst M and Saied F 1993 Multigrid solution of the Poisson-Boltzmann equation J. Comput. Chem. 14 105-13
-
(1993)
J. Comput. Chem.
, vol.14
, Issue.1
, pp. 105-113
-
-
Holst, M.1
Saied, F.2
-
32
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
DOI 10.1073/pnas.181342398
-
Baker N A, Sept D, Holst M J and McCammon J A 2001 Electrostatics of nanoysystems: application to microtubules and the ribosome Proc. Natl Acad. Sci. USA 98 10037-41 (Pubitemid 32802969)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
33
-
-
44849142209
-
The finite element approximation of the nonlinear Poisson-Boltzmann equation
-
10.1137/060675514 0036-1429
-
Chen L, Holst M J and Xu J 2007 The finite element approximation of the nonlinear Poisson-Boltzmann equation SIAM J. Numer. Anal. 45 2298-320
-
(2007)
SIAM J. Numer. Anal.
, vol.45
, Issue.6
, pp. 2298-2320
-
-
Chen, L.1
Holst, M.J.2
Xu, J.3
-
34
-
-
33749223814
-
Reevaluation of the Born model of ion hydration
-
10.1021/j100272a006 0022-3654
-
Rashin A A and Honig B 1985 Reevaluation of the Born model of ion hydration J. Phys. Chem. 89 5588-93
-
(1985)
J. Phys. Chem.
, vol.89
, Issue.26
, pp. 5588-5593
-
-
Rashin, A.A.1
Honig, B.2
-
35
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
10.1021/j100058a043 0022-3654 B
-
Sitkoff D, Sharp K A and Honig B 1994 Accurate calculation of hydration free energies using macroscopic solvent models J. Phys. Chem. B 98 1978-88
-
(1994)
J. Phys. Chem.
, vol.98
, Issue.7
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
36
-
-
0032968133
-
Implicit solvent models
-
DOI 10.1016/S0301-4622(98)00226-9, PII S0301462298002269
-
Roux B and Simonson T 1999 Implicit solvent models Biophys. Chem. 78 1-20 (Pubitemid 29206654)
-
(1999)
Biophysical Chemistry
, vol.78
, Issue.1-2
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
37
-
-
0033568644
-
Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
-
DOI 10.1021/ja990935j
-
Massova I and Kollman P A 1999 Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies J. Am. Chem. Soc. 121 8133-43 (Pubitemid 29444447)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.36
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
38
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman P A et al 2000 Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 33 889-97 (Pubitemid 32056774)
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, 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
Donini, O.11
-
39
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
10.1021/jm000241h 0022-2623
-
Kuhn B and Kollman P A 2000 Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models J. Med. Chem. 43 3786-91
-
(2000)
J. Med. Chem.
, vol.43
, Issue.20
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
40
-
-
0035892161
-
Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
-
DOI 10.1021/jp011923z
-
Tsui V and Case D A 2001 Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics J. Phys. Chem. B 105 11314-25 (Pubitemid 35338484)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.45
, pp. 11314-11325
-
-
Tsui, V.1
Case, D.A.2
-
41
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
DOI 10.1021/ja003834q
-
Wang J, Morin P, Wang W and Kollman P A 2001 Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efavirenz by docking and MM-PBSA J. Am. Chem. Soc. 123 5221-30 (Pubitemid 32910665)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.22
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
42
-
-
0037234043
-
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
-
DOI 10.1002/bip.10270
-
Gouda H, Kuntz I D, Case D A and Kollman P A 2003 Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods Biopolymers 68 16-34 (Pubitemid 36098305)
-
(2003)
Biopolymers
, vol.68
, Issue.1
, pp. 16-34
-
-
Gouda, H.1
Kuntz, I.D.2
Case, D.A.3
Kollman, P.A.4
-
43
-
-
0038650794
-
Protocol for MM/PBSA molecular dynamics simulations of proteins
-
Fogolari F, Brigo A and Molinari H 2003 Protocol for MM/PBSA molecular dynamics simulations of proteins Biophys. J. 85 159-66 (Pubitemid 36753623)
-
(2003)
Biophysical Journal
, vol.85
, Issue.1
, pp. 159-166
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
44
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
10.1002/jcc.10379 0192-8651
-
Gohlke H and Case D A 2004 Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf J. Comput. Chem. 25 238-50
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.2
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
45
-
-
0347949637
-
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
-
Swanson J M J, Henchman R H and McCammon J A 2004 Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy Biophys. J. 86 67-74 (Pubitemid 38067436)
-
(2004)
Biophysical Journal
, vol.86
, Issue.1
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
47
-
-
0001060458
-
A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution
-
10.1063/1.431685 0021-9606
-
Patey G N and Valleau J P 1975 A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution J. Chem. Phys. 63 2334-9
-
(1975)
J. Chem. Phys.
, vol.63
, Issue.6
, pp. 2334-2339
-
-
Patey, G.N.1
Valleau, J.P.2
-
48
-
-
0012587052
-
Electrical double layers. I. Monte Carlo study of a uniformly charged surface
-
10.1063/1.440065 0021-9606
-
Torrie G M and Valleau J P 1980 Electrical double layers. I. Monte Carlo study of a uniformly charged surface J. Chem. Phys. 73 5807-16
-
(1980)
J. Chem. Phys.
, vol.73
, Issue.11
, pp. 5807-5816
-
-
Torrie, G.M.1
Valleau, J.P.2
-
49
-
-
0000883906
-
Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions
-
10.1021/j100282a025 0022-3654
-
Mills P, Anderson C F T and Record M Jr 1986 Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions J. Phys. Chem. 90 6541-8
-
(1986)
J. Phys. Chem.
, vol.90
, Issue.24
, pp. 6541-6548
-
-
Mills, P.1
Anderson, C.F.T.2
Record, M.3
-
50
-
-
0024116002
-
Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials
-
10.1002/bip.360271103 0006-3525
-
Conrad J, Troll M and Zimm B H 1988 Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials Biopolymers 27 1711-32
-
(1988)
Biopolymers
, vol.27
, Issue.11
, pp. 1711-1732
-
-
Conrad, J.1
Troll, M.2
Zimm, B.H.3
-
51
-
-
33645078713
-
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
-
10.1103/PhysRevE.52.3730 1063-651X E
-
Lyubartsev A P and Laaksonen A 1995 Calculation of effective interaction potentials from radial distribution functions: a reverse Monte Carlo approach Phys. Rev. E 52 3730-7
-
(1995)
Phys. Rev.
, vol.52
, Issue.4
, pp. 3730-3737
-
-
Lyubartsev, A.P.1
Laaksonen, A.2
-
52
-
-
0000134443
-
Adsorption of proteins onto charged surfaces: A Monte Carlo approach with explicit ions
-
Juffer A H, Argos P and de Vlieg J 1996 Adsorption of proteins onto charged surfaces: a Monte Carlo approach with explicit ions J. Comput. Chem. 17 1783-803 (Pubitemid 126567061)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.16
, pp. 1783-1803
-
-
Juffer, A.H.1
Argos, P.2
De Vlieg, J.3
-
54
-
-
42749100087
-
Computing induced charges in inhomogeneous dielectric media: Application in a Monte Carlo simulation of complex ionic systems
-
10.1103/PhysRevE.69.046702 1539-3755 E 046702
-
Boda D, Gillespie D, Nonner W, Henderson D and Eisenberg B 2004 Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems Phys. Rev. E 69 046702
-
(2004)
Phys. Rev.
, vol.69
, Issue.4
-
-
Boda, D.1
Gillespie, D.2
Nonner, W.3
Henderson, D.4
Eisenberg, B.5
-
55
-
-
11144284604
-
ISIM: A program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules
-
DOI 10.1080/08927020310001597862
-
Vitalis A, Baker N A and McCammon J A 2004 ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules Mol. Simul. 30 45-61 (Pubitemid 40026348)
-
(2004)
Molecular Simulation
, vol.30
, Issue.1
, pp. 45-61
-
-
Vitalis, A.1
Baker, N.A.2
McCammon, J.A.3
-
56
-
-
33645154444
-
Monte Carlo simulations of biomolecules: The MC module in CHARMM
-
10.1002/jcc.20327 0192-8651
-
Hu J, Ma A and Dinner A R 2006 Monte Carlo simulations of biomolecules: the MC module in CHARMM J. Comput. Chem. 27 203-16
-
(2006)
J. Comput. Chem.
, vol.27
, Issue.2
, pp. 203-216
-
-
Hu, J.1
Ma, A.2
Dinner, A.R.3
-
57
-
-
64549131279
-
ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
-
10.1002/jcc.21005 0192-8651
-
Vitalis A and Pappu R V 2009 ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions J. Comput. Chem. 30 673-700
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.5
, pp. 673-700
-
-
Vitalis, A.1
Pappu, R.V.2
-
58
-
-
79961122970
-
Multiple-image treatment of induced charges in Monte Carlo simulations of electrolytes near a spherical dielectric interface
-
10.1103/PhysRevE.84.016705 1539-3755 E 016705
-
Gan Z and Xu Z 2011 Multiple-image treatment of induced charges in Monte Carlo simulations of electrolytes near a spherical dielectric interface Phys. Rev. E 84 016705
-
(2011)
Phys. Rev.
, vol.84
, Issue.1
-
-
Gan, Z.1
Xu, Z.2
-
59
-
-
0035819206
-
Monte Carlo simulations of lysozyme self-association in aqueous solution
-
DOI 10.1021/jp012235i
-
Carlsson F, Malmsten M and Linse P 2001 Monte Carlo simulations of lysozyme self-association in aqueous solution J. Phys. Chem. B 105 12189-95 (Pubitemid 35338378)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.48
, pp. 12189-12195
-
-
Carlsson, F.1
Malmsten, M.2
Linse, P.3
-
60
-
-
0035451052
-
What are the dielectric constants of proteins and how to validate electrostatic models?
-
DOI 10.1002/prot.1106
-
Schutz C N and Warshel A 2001 What are the dielectric constants of proteins and how to validate electrostatic models? Proteins 44 400-17 (Pubitemid 32768578)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.44
, Issue.4
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
61
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
10.1016/S0006-3495(00)76411-3 0006-3495
-
Dwyer J J, Gittis A G, Karp D A, Lattman E E, Spencer D S, Stites W E and García Moreno B E 2000 High apparent dielectric constants in the interior of a protein reflect water penetration Biophys. J. 79 1610-20
-
(2000)
Biophys. J.
, vol.79
, Issue.3
, pp. 1610-1620
-
-
Dwyer, J.J.1
Gittis, A.G.2
Karp, D.A.3
Lattman, E.E.4
Spencer, D.S.5
Stites, W.E.6
García Moreno, B.E.7
-
62
-
-
0029633155
-
The calculation of the potential of mean force using computer simulations
-
10.1016/0010-4655(95)00053-I 0010-4655
-
Roux B 1995 The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 275-82
-
(1995)
Comput. Phys. Commun.
, vol.91
, Issue.1-3
, pp. 275-282
-
-
Roux, B.1
-
63
-
-
0034225199
-
Electrostatic free energy calculations for macromolecules: A hybrid molecular dynamics/continuum electrostatics approach
-
10.1021/jp0014317 1520-6106 B
-
Simonson T 2000 Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach J. Phys. Chem. B 104 6509-13
-
(2000)
J. Phys. Chem.
, vol.104
, Issue.28
, pp. 6509-6513
-
-
Simonson, T.1
-
64
-
-
7544239151
-
An assessment of potential of mean force calculations with implicit solvent models
-
10.1021/jp047126t 1520-6106 B
-
Stultz C M 2004 An assessment of potential of mean force calculations with implicit solvent models J. Phys. Chem. B 108 16525-32
-
(2004)
J. Phys. Chem.
, vol.108
, Issue.42
, pp. 16525-16532
-
-
Stultz, C.M.1
-
65
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson M K, Given J A, Bush B L and McCammon J A 1997 The statistical-thermodynamic basis for computation of binding affinities: a critical review Biophys. J. 72 1047-69 (Pubitemid 27113632)
-
(1997)
Biophysical Journal
, vol.72
, Issue.3
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
66
-
-
0000101871
-
Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area
-
Hermann R B 1996 Modeling hydrophobic solvation of nonspherical systems: comparison of use of molecular surface area with accessible surface area J. Comput. Chem. 18 115-25 (Pubitemid 127599837)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.1
, pp. 115-125
-
-
Hermann, R.B.1
-
68
-
-
0042208326
-
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
-
DOI 10.1021/ja029833a
-
Levy R M, Zhang L Y, Gallicchio E and Felts A K 2003 On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy J. Am. Chem. Soc. 125 9523-30 (Pubitemid 36936069)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.31
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
-
69
-
-
0347787914
-
Continuum solvent modeling of nonpolar solvation: Improvement by separating surface area dependent cavity and dispersion contributions
-
10.1021/jp027598c 1089-5639 A
-
Zacharias M 2003 Continuum solvent modeling of nonpolar solvation: improvement by separating surface area dependent cavity and dispersion contributions J. Phys. Chem. A 107 3000-4
-
(2003)
J. Phys. Chem.
, vol.107
, Issue.16
, pp. 3000-3004
-
-
Zacharias, M.1
-
70
-
-
33750899801
-
Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial charge models and optimization of nonpolar contributions
-
10.1021/ct050097l 1549-9618
-
Rizzo R C, Aynechi T, Case D A and Kuntz I D 2006 Estimation of absolute free energies of hydration using continuum methods: accuracy of partial charge models and optimization of nonpolar contributions J. Chem. Theory Comput. 2 128-39
-
(2006)
J. Chem. Theory Comput.
, vol.2
, Issue.1
, pp. 128-139
-
-
Rizzo, R.C.1
Aynechi, T.2
Case, D.A.3
Kuntz, I.D.4
-
71
-
-
34548378695
-
Application of the level-set method to the implicit solvation of nonpolar molecules
-
DOI 10.1063/1.2757169
-
Cheng L T, Dzubiella J, McCammon J A and Li B 2007 Application of the level-set method to the implicit solvation of nonpolar molecules J. Chem. Phys. 127 084503 (Pubitemid 47352536)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.8
, pp. 084503
-
-
Cheng, L.-T.1
Dzubiella, J.2
McCammon, J.A.3
Li, B.4
-
72
-
-
65249120770
-
Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules
-
10.1021/ct800297d 1549-9618
-
Cheng L-T, Xie Y, Dzubiella J, McCammon J A, Che J and Li B 2009 Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules J. Chem. Theory Comput. 5 257-66
-
(2009)
J. Chem. Theory Comput.
, vol.5
, Issue.2
, pp. 257-266
-
-
Cheng, L.-T.1
Xie, Y.2
Dzubiella, J.3
McCammon, J.A.4
Che, J.5
Li, B.6
-
73
-
-
4444323489
-
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
-
10.1002/jcc.20089 0192-8651
-
Wagoner J and Baker N A 2004 Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models J. Comput. Chem. 25 1623-9
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.13
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.A.2
-
75
-
-
84861090702
-
Definition and computation of intermolecular contact in liquids using additively weighted voronoi tessellation
-
10.1021/jp3021886 1089-5639 A
-
Isele-Holder R E, Rabideau B D and Ismail A E 2012 Definition and computation of intermolecular contact in liquids using additively weighted voronoi tessellation J. Phys. Chem. A 116 4657-66
-
(2012)
J. Phys. Chem.
, vol.116
, Issue.18
, pp. 4657-4666
-
-
Isele-Holder, R.E.1
Rabideau, B.D.2
Ismail, A.E.3
-
76
-
-
0342817973
-
Computer solution for time-invariant electric fields
-
10.1063/1.1708789 0021-8979
-
Rush S, Turner A H and Cherin A H 1966 Computer solution for time-invariant electric fields J. Appl. Phys. 37 2211-7
-
(1966)
J. Appl. Phys.
, vol.37
, Issue.6
, pp. 2211-2217
-
-
Rush, S.1
Turner, A.H.2
Cherin, A.H.3
-
78
-
-
84946893847
-
Electrostatic interactions of a solute with a continuum - A direct utilization of ab initio molecular potentials for the provision of solvent effects
-
10.1016/0301-0104(81)85090-2 0301-0104
-
Miertus S, Scrocco E and Tomasi J 1981 Electrostatic interactions of a solute with a continuum - a direct utilization of ab initio molecular potentials for the provision of solvent effects Chem. Phys. 55 117-29
-
(1981)
Chem. Phys.
, vol.55
, Issue.1
, pp. 117-129
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
79
-
-
0001300681
-
Theory of the Poisson Green's-function for discontinuous dielectric media with an application to protein biophysics
-
10.1103/PhysRevA.32.2476 0556-2791 A
-
Shaw P B 1985 Theory of the Poisson Green's-function for discontinuous dielectric media with an application to protein biophysics Phys. Rev. A 32 2476-87
-
(1985)
Phys. Rev.
, vol.32
, Issue.4
, pp. 2476-2487
-
-
Shaw, P.B.1
-
82
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
10.1021/j100382a068 0022-3654
-
Sharp K A and Honig B 1990 Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation J. Phys. Chem. 94 7684-92
-
(1990)
J. Phys. Chem.
, vol.94
, Issue.19
, pp. 7684-7692
-
-
Sharp, K.A.1
Honig, B.2
-
83
-
-
0032968443
-
Towards a better description and understanding of biomolecular solvation
-
DOI 10.1016/S0301-4622(98)00235-X, PII S030146229800235X
-
Boresch S, Ringhofer S, Höchtl P and Steinhauser O 1999 Towards a better description and understanding of biomolecular solvation Biophys. Chem. 78 43-68 (Pubitemid 29206657)
-
(1999)
Biophysical Chemistry
, vol.78
, Issue.1-2
, pp. 43-68
-
-
Boresch, S.1
Ringhofer, S.2
Hochtl, P.3
Steinhauser, O.4
-
84
-
-
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 8678-89 (Pubitemid 126733028)
-
(1996)
Journal of Chemical Physics
, vol.104
, Issue.21
, pp. 8678-8689
-
-
Beglov, D.1
Roux, B.2
-
85
-
-
44849126646
-
The geometry behind numerical solvers of the Poisson-Boltzmann equation
-
1815-2406
-
Shi X and Koehl P 2008 The geometry behind numerical solvers of the Poisson-Boltzmann equation Commun. Comput. Phys. 3 1032-50 (available at http://www.global-sci.com/issue/contents/3/issue5.html)
-
(2008)
Commun. Comput. Phys.
, vol.3
, pp. 1032-1050
-
-
Shi, X.1
Koehl, P.2
-
86
-
-
0020475509
-
Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
-
10.1016/0022-2836(82)90505-8 0022-2836
-
Warwicker J and Watson H C 1982 Calculation of the electric potential in the active site cleft due to alpha-helix dipoles J. Mol. Biol. 157 671-9
-
(1982)
J. Mol. Biol.
, vol.157
, Issue.4
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
87
-
-
0021813940
-
On the calculation of electrostatic interactions in proteins
-
DOI 10.1016/0022-2836(85)90297-9
-
Gilson M K, Rashin A, Fine R and Honig B 1985 On the calculation of electrostatic interactions in proteins J. Mol. Biol. 184 503-16 (Pubitemid 15013023)
-
(1985)
Journal of Molecular Biology
, vol.184
, Issue.3
, pp. 503-516
-
-
Gilson, M.K.1
Rashin, A.2
Fine, R.3
Honig, B.4
-
88
-
-
0022964504
-
Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
-
DOI 10.1002/prot.340010109
-
Klapper I, Hagstrom R, Fine R, Sharp K and Honig B 1986 Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification Proteins 1 47-59 (Pubitemid 17073401)
-
(1986)
Proteins: Structure, Function and Genetics
, vol.1
, Issue.1
, pp. 47-59
-
-
Klapper, I.1
Hagstrom, R.2
Fine, R.3
-
89
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
10.1002/jcc.540090407 0192-8651
-
Gilson M K, Sharp K A and Honig B H 1988 Calculating the electrostatic potential of molecules in solution: method and error assessment J. Comput. Chem. 9 327-35
-
(1988)
J. Comput. Chem.
, vol.9
, Issue.4
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
90
-
-
84986486656
-
A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
10.1002/jcc.540120405 0192-8651
-
Nicholls A and Honig B 1991 A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J. Comput. Chem. 12 435-45
-
(1991)
J. Comput. Chem.
, vol.12
, Issue.4
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
91
-
-
0000682989
-
Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing
-
Bruccoleri R E, Novotny J, Davis M E and Sharp K A 1996 Finite difference Poisson-Boltzmann electrostatic calculations: increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing J. Comput. Chem. 18 268-76 (Pubitemid 127598571)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.2
, pp. 268-276
-
-
Bruccoleri, R.E.1
Novotny, J.2
Davis, M.E.3
Sharp, K.A.4
-
92
-
-
85033849708
-
Finite-difference solution of the Poisson - Boltzmann equation: Complete elimination of self-energy
-
Zhou Z X, Payne P, Vasquez M, Kuhn N and Levitt M 1996 Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy J. Comput. Chem. 17 1344-51 (Pubitemid 126576751)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.11
, pp. 1344-1351
-
-
Zhou, Z.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
-
93
-
-
0027379329
-
The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems
-
Pack G R, Garrett G A, Wong L and Lamm G 1993 The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems Biophys. J. 65 1363-70 (Pubitemid 23316955)
-
(1993)
Biophysical Journal
, vol.65
, Issue.4
, pp. 1363-1370
-
-
Pack, G.R.1
Garrett, G.A.2
Wong, L.3
Lamm, G.4
-
94
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
DOI 10.1021/jp010454y
-
Rocchia W, Alexov E and Honig B 2001 Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J. Phys. Chem. B 105 6507-14 (Pubitemid 35339019)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
95
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
DOI 10.1002/jcc.10120
-
Luo R, David L and Gilson M K 2002 Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 23 1244-53 (Pubitemid 35009216)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.13
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
96
-
-
0347410858
-
A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
-
10.1063/1.1622376 0021-9606
-
Lu Q and Luo R 2003 A Poisson-Boltzmann dynamics method with nonperiodic boundary condition J. Chem. Phys 119 11035-47
-
(2003)
J. Chem. Phys
, vol.119
, Issue.21
, pp. 11035-11047
-
-
Lu, Q.1
Luo, R.2
-
97
-
-
44849141672
-
Poisson-Boltzmann solvents in molecular dynamics simulations
-
1815-2406
-
Wang J, Tan C, Tan Y-H, Lu Q and Luo R 2008 Poisson-Boltzmann solvents in molecular dynamics simulations Commun. Comput. Phys. 3 1010-31 (available at http://www.global-sci.com/issue/contents/3/issue5.html)
-
(2008)
Commun. Comput. Phys.
, vol.3
, pp. 1010-1031
-
-
Wang, J.1
Tan, C.2
Tan, Y.-H.3
Lu, Q.4
Luo, R.5
-
98
-
-
77951102912
-
A revised density function for molecular surface calculation in continuum solvent models
-
10.1021/ct900318u 1549-9618
-
Ye X, Wang J and Luo R 2010 A revised density function for molecular surface calculation in continuum solvent models J. Chem. Theory Comput. 6 1157-69
-
(2010)
J. Chem. Theory Comput.
, vol.6
, Issue.4
, pp. 1157-1169
-
-
Ye, X.1
Wang, J.2
Luo, R.3
-
99
-
-
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
-
DOI 10.1002/jcc.1161
-
Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A and Honig B 2002 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. 23 128-37 (Pubitemid 34063137)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.1
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
100
-
-
34648817162
-
Treatment of charge singularities in implicit solvent models
-
DOI 10.1063/1.2768064
-
Geng W H, Yu S N and Wei G W 2007 Treatment of charge singularities in implicit solvent models J. Chem. Phys. 127 114106 (Pubitemid 47461993)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.11
, pp. 114106
-
-
Wei, G.1
Geng, W.2
Yu, S.3
-
101
-
-
34547352376
-
Treatment of geometric singularities in implicit solvent models
-
DOI 10.1063/1.2743020
-
Yu S N, Geng W H and Wei G W 2007 Treatment of geometric singularities in implicit solvent models J. Chem. Phys. 126 244108 (Pubitemid 47141404)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.24
, pp. 244108
-
-
Yu, S.1
Geng, W.2
Wei, G.W.3
-
102
-
-
65249120173
-
On removal of charge singularity in Poisson-Boltzmann equation
-
10.1063/1.3099708 0021-9606 145101
-
Cai Q, Wang J, Zhao H-K and Luo R 2009 On removal of charge singularity in Poisson-Boltzmann equation J. Chem. Phys. 130 145101
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.14
-
-
Cai, Q.1
Wang, J.2
Zhao, H.-K.3
Luo, R.4
-
103
-
-
37649005586
-
Highly accurate biomolecular electrostatics in continuum dielectric environments
-
10.1002/jcc.20769 0192-8651
-
Zhou Y C, Feig M and Wei G W 2008 Highly accurate biomolecular electrostatics in continuum dielectric environments J. Comput. Chem. 29 87-97
-
(2008)
J. Comput. Chem.
, vol.29
, Issue.1
, pp. 87-97
-
-
Zhou, Y.C.1
Feig, M.2
Wei, G.W.3
-
104
-
-
79251528566
-
MIBPB: A software package for electrostatic analysis
-
10.1002/jcc.21646 0192-8651
-
Chen D, Chen Z, Chen C, Geng W and Wei G-W 2010 MIBPB: a software package for electrostatic analysis J. Comput. Chem. 32 756-70
-
(2010)
J. Comput. Chem.
, vol.32
, Issue.4
, pp. 756-770
-
-
Chen, D.1
Chen, Z.2
Chen, C.3
Geng, W.4
Wei, G.-W.5
-
105
-
-
77950180193
-
Performance of nonlinear finite-difference Poisson-Boltzmann solvers
-
10.1021/ct900381r 1549-9618
-
Cai Q, Hsieh M-J, Wang J and Luo R 2010 Performance of nonlinear finite-difference Poisson-Boltzmann solvers J. Chem. Theory Comput. 6 203-11
-
(2010)
J. Chem. Theory Comput.
, vol.6
, Issue.1
, pp. 203-211
-
-
Cai, Q.1
Hsieh, M.-J.2
Wang, J.3
Luo, R.4
-
107
-
-
84055193468
-
Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
-
1815-2406
-
Holst M, McCammon J A, Yu Z, Zhou Y C and Zhu Y 2012 Adaptive finite element modeling techniques for the Poisson-Boltzmann equation Commun. Comput. Phys. 11 179-214 (available at http://www.global-sci.com/issue/contents/11/ issue1.html)
-
(2012)
Commun. Comput. Phys.
, vol.11
, pp. 179-214
-
-
Holst, M.1
McCammon, J.A.2
Yu, Z.3
Zhou, Y.C.4
Zhu, Y.5
-
108
-
-
77955272371
-
Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes: I. Finite element solutions
-
10.1016/j.jcp.2010.05.035 0021-9991
-
Lu B, Holst M J, McCammon J A and Zhou Y C 2010 Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes: I. Finite element solutions J. Comput. Phys. 229 6979-94
-
(2010)
J. Comput. Phys.
, vol.229
, Issue.19
, pp. 6979-6994
-
-
Lu, B.1
Holst, M.J.2
McCammon, J.A.3
Zhou, Y.C.4
-
109
-
-
84962378412
-
-
Holst M J 1993 Multilevel methods for the Poisson-Boltzmann equation PhD Thesis University of Illinois Press, Champaign, IL
-
(1993)
PhD Thesis
-
-
Holst, M.J.1
-
110
-
-
0001007983
-
Finite-element approach to the electrostatics of macromolecules with arbitrary geometries
-
10.1002/jcc.540140413 0192-8651
-
You T J and Harvey S C 1993 Finite-element approach to the electrostatics of macromolecules with arbitrary geometries J. Comput. Chem. 14 484-501
-
(1993)
J. Comput. Chem.
, vol.14
, Issue.4
, pp. 484-501
-
-
You, T.J.1
Harvey, S.C.2
-
111
-
-
0030777609
-
Adaptive finite-element: Solution of the nonlinear Poisson-Boltzmann equation: A charged spherical particle at various distances from a charged cylindrical pore in a charged planar surface
-
DOI 10.1006/jcis.1996.4705
-
Bowen W R and Sharif A O 1997 Adaptive finite-element solution of the nonlinear Poisson-Boltzmann equation: a charged spherical particle at various distances from a charged cylindrical pore in a charged planar surface J. Colloid Interface Sci. 187 363-74 (Pubitemid 27470952)
-
(1997)
Journal of Colloid and Interface Science
, vol.187
, Issue.2
, pp. 363-374
-
-
Bowen, W.R.1
Sharif, A.O.2
-
112
-
-
0001620743
-
An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation
-
Cortis C M and Friesner R A 1997 An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation J. Comput. Chem. 18 1570-90 (Pubitemid 127677975)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.13
, pp. 1570-1590
-
-
Cortis, C.M.1
Friesner, R.A.2
-
113
-
-
0001439211
-
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
-
Cortis C M and Friesner R A 1997 Numerical simulation of the Poisson-Boltzmann equation using tetrahedral finite-element meshes J. Comput. Chem. 18 1591-608 (Pubitemid 127677976)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.13
, pp. 1591-1608
-
-
Cortis, C.M.1
Friesner, R.A.2
-
114
-
-
0000486194
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: II. Refinement at solvent-accessible surfaces in biomolecular systems
-
10.1002/1096-987X(20001130)21:15<1343::AID-JCC2>3.0.CO;2-K 0192-8651
-
Baker N, Holst M and Wang F 2000 Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: II. Refinement at solvent-accessible surfaces in biomolecular systems J. Comput. Chem. 21 1343-52
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.15
, pp. 1343-1352
-
-
Baker, N.1
Holst, M.2
Wang, F.3
-
115
-
-
0000486193
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: I. Algorithms and examples
-
10.1002/1096-987X(20001130)21:15<1319::AID-JCC1>3.0.CO;2-8 0192-8651
-
Holst M, Baker N and Wang F 2000 Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: I. Algorithms and examples J. Comput. Chem. 21 1319-42
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.15
, pp. 1319-1342
-
-
Holst, M.1
Baker, N.2
Wang, F.3
-
116
-
-
42749086211
-
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation
-
10.1016/j.jmgm.2008.01.007 1093-3263
-
Yu Z, Holst M J, Cheng Y and McCammon J A 2008 Feature-preserving adaptive mesh generation for molecular shape modeling and simulation J. Mol. Graph. Model. 26 1370-80
-
(2008)
J. Mol. Graph. Model.
, vol.26
, Issue.8
, pp. 1370-1380
-
-
Yu, Z.1
Holst, M.J.2
Cheng, Y.3
McCammon, J.A.4
-
117
-
-
79952900041
-
A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid
-
10.1016/j.jcp.2011.02.010 0021-9991
-
Helgadóttir A and Gibou F 2011 A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid J. Comput. Phys. 230 3830-48
-
(2011)
J. Comput. Phys.
, vol.230
, Issue.10
, pp. 3830-3848
-
-
Helgadóttir, A.1
Gibou, F.2
-
118
-
-
77952378191
-
A first-order system least-squares finite element method for the Poisson-Boltzmann equation
-
Bond S D, Chaudhry J H, Cyr E C and Olson L N 2010 A first-order system least-squares finite element method for the Poisson-Boltzmann equation J. Comput. Chem. 31 1625-35
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1625-1635
-
-
Bond, S.D.1
Chaudhry, J.H.2
Cyr, E.C.3
Olson, L.N.4
-
119
-
-
0000396658
-
A fast algorithm for particle simulations
-
10.1016/0021-9991(87)90140-9 0021-9991
-
Greengard L and Rokhlin V 1987 A fast algorithm for particle simulations J. Comput. Phys. 73 325-48
-
(1987)
J. Comput. Phys.
, vol.73
, Issue.2
, pp. 325-348
-
-
Greengard, L.1
Rokhlin, V.2
-
120
-
-
0032117876
-
Accelerating fast multipole methods for the Helmholtz equation at low frequencies
-
10.1109/99.714591 1070-9924
-
Greengard L, Huang J, Rokhlin V and Wandzura S 1998 Accelerating fast multipole methods for the Helmholtz equation at low frequencies IEEE Comput. Sci. Eng. 5 32-8
-
(1998)
IEEE Comput. Sci. Eng.
, vol.5
, Issue.3
, pp. 32-38
-
-
Greengard, L.1
Huang, J.2
Rokhlin, V.3
Wandzura, S.4
-
121
-
-
0000362580
-
A fast adaptive multipole algorithm in three dimensions
-
10.1006/jcph.1999.6355 0021-9991
-
Cheng H, Greengard L and Rokhlin V 1999 A fast adaptive multipole algorithm in three dimensions J. Comput. Phys. 155 468-98
-
(1999)
J. Comput. Phys.
, vol.155
, Issue.2
, pp. 468-498
-
-
Cheng, H.1
Greengard, L.2
Rokhlin, V.3
-
122
-
-
0000687899
-
An Adaptive Treecode for Computing Nonbonded Potential Energy in Classical Molecular Systems
-
DOI 10.1002/1096-987X(20010130)22:2<184::AID-JCC6>3.0.CO;2-7
-
Duan Z-H and Krasny R 2001 An adaptive treecode for computing nonbonded potential energy in classical molecular systems J. Comput. Chem. 22 184-95 (Pubitemid 33646623)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.2
, pp. 184-195
-
-
Duan, Z.-H.1
Krasny, R.2
-
124
-
-
77951687164
-
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries
-
10.1063/1.3376011 0021-9606 154112
-
Tyagi S, Süzen M, Sega M, Barbosa M, Kantorovich S S and Holm C 2010 An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries J. Chem. Phys. 132 154112
-
(2010)
J. Chem. Phys.
, vol.132
, Issue.15
-
-
Tyagi, S.1
Süzen, M.2
Sega, M.3
Barbosa, M.4
Kantorovich, S.S.5
Holm, C.6
-
126
-
-
2442446356
-
A kernel-independent adaptive fast multipole algorithm in two and three dimensions
-
DOI 10.1016/j.jcp.2003.11.021
-
Ying L, Biros G and Zorin D 2004 A kernel-independent adaptive fast multipole algorithm in two and three dimensions J. Comput. Phys. 196 591-626 (Pubitemid 38613258)
-
(2004)
Journal of Computational Physics
, vol.196
, Issue.2
, pp. 591-626
-
-
Ying, L.1
Biros, G.2
Zorin, D.3
-
130
-
-
0000048673
-
GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems
-
10.1137/0907058 0196-5204
-
Saad Y and Schultz M 1986 GMRES: a generalized minimal residual algorithm for solving nonsymmetric linear systems SIAM J. Sci. Stat. Comput. 7 856-69
-
(1986)
SIAM J. Sci. Stat. Comput.
, vol.7
, Issue.3
, pp. 856-869
-
-
Saad, Y.1
Schultz, M.2
-
131
-
-
62249173004
-
Numerical solution of boundary-integral equations for molecular electrostatics
-
10.1063/1.3080769 0021-9606 094102
-
Bardhan J P 2009 Numerical solution of boundary-integral equations for molecular electrostatics J. Chem. Phys. 130 094102
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.9
-
-
Bardhan, J.P.1
-
132
-
-
84986435825
-
Remarks on the apparent-surface charges (ASC) methods in solvation problems: Iterative versus matrix-inversion procedures and the renormalization of the apparent charges
-
10.1002/jcc.540161202 0192-8651
-
Cammi R and Tomasi J 1995 Remarks on the apparent-surface charges (ASC) methods in solvation problems: iterative versus matrix-inversion procedures and the renormalization of the apparent charges J. Comput. Chem. 16 1449-58
-
(1995)
J. Comput. Chem.
, vol.16
, Issue.12
, pp. 1449-1458
-
-
Cammi, R.1
Tomasi, J.2
-
133
-
-
84962460748
-
Discretization of the induced-charge boundary integral equation
-
10.1103/PhysRevE.80.011906 1539-3755 E 011906
-
Bardhan J P, Eisenberg R S and Gillespie D 2009 Discretization of the induced-charge boundary integral equation Phys. Rev. E 80 011906
-
(2009)
Phys. Rev.
, vol.80
, Issue.1
-
-
Bardhan, J.P.1
Eisenberg, R.S.2
Gillespie, D.3
-
134
-
-
0034863617
-
Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide
-
DOI 10.1002/1097-0282(2001)60:2<124::AID-BIP1008>3.0.CO;2-S
-
Totrov M and Abagyan R 2001 Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide Biopolymers 60 124-33 (Pubitemid 32743529)
-
(2001)
Biopolymers - Peptide Science Section
, vol.60
, Issue.2
, pp. 124-133
-
-
Totrov, M.1
Abagyan, R.2
-
135
-
-
0031560531
-
Incorporating hydration force determined by boundary element method into stochastic dynamics
-
Wang C X, Wan S Z, Xiang Z X and Shi Y Y 1997 Incorporating hydration force determined by boundary element method into stochastic dynamics J. Phys. Chem. B 101 230-5 (Pubitemid 127627847)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.2
, pp. 230-235
-
-
Wang, C.X.1
Wan, S.Z.2
Xiang, Z.X.3
Shi, Y.Y.4
-
136
-
-
84961981995
-
Comparison of solvent reaction field representations
-
DOI 10.1007/s00214-001-0302-1
-
Chipman D N 2002 Comparison of solvent reaction field representations Theor. Chem. Acc. 107 80-9 (Pubitemid 40835028)
-
(2002)
Theoretical Chemistry Accounts
, vol.107
, Issue.2
, pp. 80-89
-
-
Chipman, D.M.1
-
137
-
-
1942471026
-
Solution of the linearized Poisson-Boltzmann equation
-
10.1063/1.1648632 0021-9606
-
Chipman D M 2004 Solution of the linearized Poisson-Boltzmann equation J. Chem. Phys. 120 5566-75
-
(2004)
J. Chem. Phys.
, vol.120
, Issue.12
, pp. 5566-5575
-
-
Chipman, D.M.1
-
138
-
-
36549100321
-
Medium effects on the molecular electronic-structure: I. The formulation of a theory for the estimation of a molecular electronic-structure surrounded by an anisotropic medium
-
10.1063/1.453343 0021-9606
-
Hoshi H, Sakurai M, Inoue Y and Chuûjô R 1987 Medium effects on the molecular electronic-structure: I. The formulation of a theory for the estimation of a molecular electronic-structure surrounded by an anisotropic medium J. Chem. Phys. 87 1107-15
-
(1987)
J. Chem. Phys.
, vol.87
, Issue.2
, pp. 1107-1115
-
-
Hoshi, H.1
Sakurai, M.2
Inoue, Y.3
Chuûjô, R.4
-
139
-
-
0031209054
-
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to Isotropic and anisotropic dielectrics
-
Cances E, Mennucci B and Tomasi J 1997 A new integral equation formalism for the polarizable continuum model: theoretical background and applications to isotropic and anisotropic dielectrics J. Chem. Phys. 107 3032-41 (Pubitemid 127568923)
-
(1997)
Journal of Chemical Physics
, vol.107
, Issue.8
, pp. 3032-3041
-
-
Cances, E.1
Mennucci, B.2
Tomasi, J.3
-
140
-
-
0031553301
-
Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: Theoretical bases, computational implementation, and numerical applications
-
Mennucci B, Cancès E and Tomasi J 1997 Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: theoretical bases, computational implementation and numerical applications J. Phys. Chem. B 101 10506-17 (Pubitemid 127587741)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.49
, pp. 10506-10517
-
-
Mennucci, B.1
Cances, E.2
Tomasi, J.3
-
141
-
-
70449378690
-
First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent
-
10.1063/1.3254385 0021-9606 174108
-
Sánchez V M, Sued M and Scherlis D A 2009 First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent J. Chem. Phys. 131 174108
-
(2009)
J. Chem. Phys.
, vol.131
, Issue.17
-
-
Sánchez, V.M.1
Sued, M.2
Scherlis, D.A.3
-
142
-
-
0022429751
-
A new method for computing the macromolecular electric-potential
-
10.1016/0022-2836(85)90399-7 0022-2836
-
Zauhar R J and Morgan R S 1985 A new method for computing the macromolecular electric-potential J. Mol. Biol. 186 815-20
-
(1985)
J. Mol. Biol.
, vol.186
, Issue.4
, pp. 815-820
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
143
-
-
84988110397
-
The rigorous computation of the molecular electric potential
-
10.1002/jcc.540090209 0192-8651
-
Zauhar R J and Morgan R S 1988 The rigorous computation of the molecular electric potential J. Comput. Chem. 9 171-87
-
(1988)
J. Comput. Chem.
, vol.9
, Issue.2
, pp. 171-187
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
144
-
-
84986465557
-
Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation
-
10.1002/jcc.540110509 0192-8651
-
Zauhar R J and Morgan R S 1990 Computing the electric potential of biomolecules: application of a new method of molecular surface triangulation J. Comput. Chem. 11 603-22
-
(1990)
J. Comput. Chem.
, vol.11
, Issue.5
, pp. 603-622
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
145
-
-
0029286072
-
SMART: A solvent-accessible triangulated surface generator for molecular graphics and boundary-element applications
-
10.1007/BF00124405 0920-654X
-
Zauhar R J 1995 SMART: a solvent-accessible triangulated surface generator for molecular graphics and boundary-element applications J. Comput. - Aided Mol. Des. 9 149-59
-
(1995)
J. Comput. - Aided Mol. Des.
, vol.9
, Issue.2
, pp. 149-159
-
-
Zauhar, R.J.1
-
146
-
-
0000482651
-
Hydrodynamic friction and the capacitance of arbitrarily shaped objects
-
10.1103/PhysRevE.49.5319 1063-651X E
-
Douglas J F, Zhou H-X and Hubbard J B 1994 Hydrodynamic friction and the capacitance of arbitrarily shaped objects Phys. Rev. E 49 5319-31
-
(1994)
Phys. Rev.
, vol.49
, Issue.6
, pp. 5319-5331
-
-
Douglas, J.F.1
Zhou, H.-X.2
Hubbard, J.B.3
-
147
-
-
33845281231
-
A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes
-
10.1021/j100307a038 0022-3654
-
Rashin A A and Namboodiri K 1987 A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes J. Phys. Chem. 91 6003-12
-
(1987)
J. Phys. Chem.
, vol.91
, Issue.23
, pp. 6003-6012
-
-
Rashin, A.A.1
Namboodiri, K.2
-
148
-
-
26844574873
-
Hydration phenomena, classical electrostatics and the boundary element method
-
10.1021/j100368a005 0022-3654
-
Rashin A A 1990 Hydration phenomena, classical electrostatics and the boundary element method J. Phys. Chem. 94 1725-33
-
(1990)
J. Phys. Chem.
, vol.94
, Issue.5
, pp. 1725-1733
-
-
Rashin, A.A.1
-
149
-
-
84962433790
-
Boundary integral methods for the poisson equation of continuum dielectric solvation models
-
Pratt L R, Tawa G J, Hummer G, Garcia A E and Corcelli S A 1997 Boundary integral methods for the Poisson equation of continuum dielectric solvation models Int. J. Quantum Chem. 64 121-41 (Pubitemid 127622033)
-
(1997)
International Journal of Quantum Chemistry
, vol.64
, Issue.1
, pp. 121-141
-
-
Pratt, L.R.1
Tawa, G.J.2
Hummer, G.3
Garcia, A.E.4
Corcelli, S.A.5
-
150
-
-
0027254625
-
Boundary-element solution of macromolecular electrostatics - Interaction energy between 2 proteins
-
10.1016/S0006-3495(93)81094-4 0006-3495
-
Zhou H X 1993 Boundary-element solution of macromolecular electrostatics - interaction energy between 2 proteins Biophys. J. 65 955-63
-
(1993)
Biophys. J.
, vol.65
, Issue.2
, pp. 955-963
-
-
Zhou, H.X.1
-
151
-
-
84986456126
-
A simple yet accurate boundary-element method for continuum dielectric calculations
-
10.1002/jcc.540160604 0192-8651
-
Purisima E O and Nilar S H 1995 A simple yet accurate boundary-element method for continuum dielectric calculations J. Comput. Chem. 16 681-9
-
(1995)
J. Comput. Chem.
, vol.16
, Issue.6
, pp. 681-689
-
-
Purisima, E.O.1
Nilar, S.H.2
-
152
-
-
0005652597
-
Fast summation boundary element method for calculating solvation free energies of macromolecules
-
Purisima E O 1998 Fast summation boundary element method for calculating solvation free energies of macromolecules J. Comput. Chem. 19 1494-504 (Pubitemid 128592640)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.13
, pp. 1494-1504
-
-
Purisima, E.O.1
-
153
-
-
0025612447
-
Ab initio self-consistent field and potential dependent partial equalization of orbital electronegativity calculations of hydration properties of n-acetyl-n'-methyl-alanineamide
-
10.1002/bip.360300908 0006-3525
-
Grant J A, Williams R L and Scheraga H A 1990 Ab initio self-consistent field and potential dependent partial equalization of orbital electronegativity calculations of hydration properties of n-acetyl-n'-methyl-alanineamide Biopolymers 30 929-49
-
(1990)
Biopolymers
, vol.30
, Issue.9-10
, pp. 929-949
-
-
Grant, J.A.1
Williams, R.L.2
Scheraga, H.A.3
-
154
-
-
0001547345
-
A combined iterative and boundary element approach for solution of the nonlinear Poisson-Boltzmann equation
-
10.1021/ja00035a003 0002-7863
-
Vorobjev Y N, Grant J A and Scheraga H A 1992 A combined iterative and boundary element approach for solution of the nonlinear Poisson-Boltzmann equation J. Am. Chem. Soc. 114 3189-96
-
(1992)
J. Am. Chem. Soc.
, vol.114
, Issue.9
, pp. 3189-3196
-
-
Vorobjev, Y.N.1
Grant, J.A.2
Scheraga, H.A.3
-
155
-
-
0010924035
-
Interaction of a biomolecule with ions in aqueous solution: Comparison of three fast approximate methods with the direct solution of the nonlinear Poisson-Boltzmann equation
-
10.1021/j100120a044 0022-3654
-
Vorobjev Y N and Scheraga H A 1993 Interaction of a biomolecule with ions in aqueous solution: comparison of three fast approximate methods with the direct solution of the nonlinear Poisson-Boltzmann equation J. Phys. Chem. 97 4855-64
-
(1993)
J. Phys. Chem.
, vol.97
, Issue.18
, pp. 4855-4864
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
156
-
-
0001445346
-
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
-
Vorobjev Y N and Scheraga H A 1997 A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent J. Comput. Chem. 18 569-83 (Pubitemid 127780803)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.4
, pp. 569-583
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
157
-
-
0030793507
-
SIMS: Computation of a smooth invariant molecular surface
-
Vorobjev Y N and Hermans J 1997 SIMS: computation of a smooth invariant molecular surface Biophys. J. 73 722-32 (Pubitemid 27337607)
-
(1997)
Biophysical Journal
, vol.73
, Issue.2
, pp. 722-732
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
158
-
-
84986452939
-
The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
-
10.1002/jcc.540160707 0192-8651
-
Bharadwaj R, Windemuth A, Sridharan S, Honig B and Nicholls A 1995 The fast multipole boundary element method for molecular electrostatics: an optimal approach for large systems J. Comput. Chem. 16 898-913
-
(1995)
J. Comput. Chem.
, vol.16
, Issue.7
, pp. 898-913
-
-
Bharadwaj, R.1
Windemuth, A.2
Sridharan, S.3
Honig, B.4
Nicholls, A.5
-
159
-
-
84962478456
-
A boundary element method for molecular electrostatics with electrolyte effects
-
10.1002/jcc.540110911 0192-8651
-
Yoon B J and Lenhoff A M 1990 A boundary element method for molecular electrostatics with electrolyte effects J. Comput. Chem. 11 1080-6
-
(1990)
J. Comput. Chem.
, vol.11
, Issue.9
, pp. 1080-1086
-
-
Yoon, B.J.1
Lenhoff, A.M.2
-
160
-
-
0002334742
-
The electric potential of a macromolecule in a solvent: A fundamental approach
-
10.1016/0021-9991(91)90043-K 0021-9991
-
Juffer A H, Botta E F F, van Keulen B A M, van der Ploeg A and Berendsen H J C 1991 The electric potential of a macromolecule in a solvent: a fundamental approach J. Comput. Phys. 97 144-71
-
(1991)
J. Comput. Phys.
, vol.97
, Issue.1
, pp. 144-171
-
-
Juffer, A.H.1
Botta, E.F.F.2
Van Keulen, B.A.M.3
Van Der Ploeg, A.4
Berendsen, H.J.C.5
-
161
-
-
0037328258
-
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
-
10.1002/jcc.10195 0192-8651
-
Bordner A J and Huber G A 2003 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. 24 353-67
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.3
, pp. 353-367
-
-
Bordner, A.J.1
Huber, G.A.2
-
162
-
-
34249284494
-
A rapid boundary integral equation technique for protein electrostatics
-
10.1016/j.jcp.2006.10.021 0021-9991
-
Grandison S, Penfold R and Vanden-Broeck J-M 2007 A rapid boundary integral equation technique for protein electrostatics J. Comput. Phys. 224 663-80
-
(2007)
J. Comput. Phys.
, vol.224
, Issue.2
, pp. 663-680
-
-
Grandison, S.1
Penfold, R.2
Vanden-Broeck, J.-M.3
-
163
-
-
0031161832
-
Charge penetration in dielectric models of solvation
-
Chipman D M 1997 Charge penetration in dielectric models of solvation J. Chem. Phys. 106 10194-206 (Pubitemid 127626981)
-
(1997)
Journal of Chemical Physics
, vol.106
, Issue.24
, pp. 10194-10206
-
-
Chipman, D.M.1
-
164
-
-
84962379036
-
Volume polarization in reaction field theory
-
10.1063/1.475371 0021-9606
-
Zhan C-G, Bentley J and Chipman D M 1998 Volume polarization in reaction field theory J. Chem. Phys. 108 177
-
(1998)
J. Chem. Phys.
, vol.108
, Issue.1
, pp. 177
-
-
Zhan, C.-G.1
Bentley, J.2
Chipman, D.M.3
-
165
-
-
84962360784
-
A new boundary integral equation for molecular electrostatics with charges over whole space
-
10.1007/s10543-011-0329-1 0006-3835
-
Xie D and Scott L R 2011 A new boundary integral equation for molecular electrostatics with charges over whole space BIT Numer. Math. 51 1-21
-
(2011)
BIT Numer. Math.
, vol.51
, Issue.4
, pp. 1051-1121
-
-
Xie, D.1
Scott, L.R.2
-
166
-
-
0001445346
-
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
-
Vorobjev Y N and Scheraga H A 1997 A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent J. Comput. Chem. 18 569-83 (Pubitemid 127780803)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.4
, pp. 569-583
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
167
-
-
0343881269
-
Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA
-
Fenley M O, Olson W K, Chua K and Boschitsch A H 1996 Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA J. Comput. Chem. 17 976-91 (Pubitemid 126572058)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.8
, pp. 976-991
-
-
Fenley, M.O.1
Olson, W.K.2
Chua, K.3
Boschitsch, A.H.4
-
168
-
-
0003111075
-
A fast adaptive multipole algorithm for calculating screened Coulomb (Yukawa) interactions
-
10.1006/jcph.1998.6176 0021-9991
-
Boschitsch A H, Fenley M O and Olson W K 1999 A fast adaptive multipole algorithm for calculating screened Coulomb (Yukawa) interactions J. Comput. Phys. 151 212-41
-
(1999)
J. Comput. Phys.
, vol.151
, Issue.1
, pp. 212-241
-
-
Boschitsch, A.H.1
Fenley, M.O.2
Olson, W.K.3
-
169
-
-
0037076079
-
Fast boundary element method for the linear Poisson-Boltzmann equation
-
DOI 10.1021/jp013607q
-
Boschitsch A H, Fenley M O and Zhou H-X 2002 Fast boundary element method for the linear Poisson-Boltzmann equation J. Phys. Chem. B 106 2741-54 (Pubitemid 35275953)
-
(2002)
Journal of Physical Chemistry B
, vol.106
, Issue.10
, pp. 2741-2754
-
-
Boschitsch, A.H.1
Fenley, M.O.2
Zhou, H.-X.3
-
170
-
-
0037055750
-
A new version of the fast multipole method for screened coulomb interactions in three dimensions
-
10.1006/jcph.2002.7110 0021-9991
-
Greengard L and Huang J 2002 A new version of the fast multipole method for screened coulomb interactions in three dimensions J. Comput. Phys. 180 642-58
-
(2002)
J. Comput. Phys.
, vol.180
, Issue.2
, pp. 642-658
-
-
Greengard, L.1
Huang, J.2
-
172
-
-
21244431972
-
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method
-
DOI 10.1063/1.1924448, 214102
-
Lu B Z, Zhang D Q and McCammon J A 2005 Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method J. Chem. Phys. 122 214102 (Pubitemid 40890496)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.21
, pp. 1-7
-
-
Lu, B.1
Zhang, D.2
McCammon, J.A.3
-
174
-
-
58149235261
-
Accurate solution of multi-region continuum electrostatic problems using the linearized Poisson-Boltzmann equation and curved boundary elements
-
10.1002/jcc.21027 0192-8651
-
Altman M D, Bardhan J P, White J K and Tidor B 2009 Accurate solution of multi-region continuum electrostatic problems using the linearized Poisson-Boltzmann equation and curved boundary elements J. Comput. Chem. 30 132-53
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.1
, pp. 132-153
-
-
Altman, M.D.1
Bardhan, J.P.2
White, J.K.3
Tidor, B.4
-
175
-
-
16844371628
-
A fast direct solver for boundary integral equations in two dimensions
-
10.1016/j.jcp.2004.10.033 0021-9991
-
Martinsson P-G and Rokhlin V 2005 A fast direct solver for boundary integral equations in two dimensions J. Comput. Phys. 205 1-23
-
(2005)
J. Comput. Phys.
, vol.205
, Issue.1
, pp. 1-23
-
-
Martinsson, P.-G.1
Rokhlin, V.2
-
176
-
-
77949624887
-
Fast direct solvers for integral equations in complex three-dimensional domains
-
10.1017/S0962492906410011 0962-4929
-
Greengard L, Gueyffier D, Martinsson P-G and Rokhlin V 2009 Fast direct solvers for integral equations in complex three-dimensional domains Acta Numer. 18 243-75
-
(2009)
Acta Numer.
, vol.18
, pp. 243-275
-
-
Greengard, L.1
Gueyffier, D.2
Martinsson, P.-G.3
Rokhlin, V.4
-
177
-
-
84869743113
-
A fast direct solver for structured linear systems by recursive skeletonization
-
10.1137/120866683 1064-8275
-
Ho K L and Greengard L 2011 A fast direct solver for structured linear systems by recursive skeletonization SIAM J. Sci. Comput. 34 A2507-32
-
(2011)
SIAM J. Sci. Comput.
, vol.34
, Issue.5
-
-
Ho, K.L.1
Greengard, L.2
-
178
-
-
0031237025
-
Calculating acid-dissociation constants of proteins using the boundary element method
-
Juffer A H, Argos P and Vogel H J 1997 Calculating acid-dissociation constants using the boundary element method J. Phys. Chem. B 101 7664-73 (Pubitemid 127581215)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.38
, pp. 7664-7673
-
-
Juffer, A.H.1
Argos, P.2
Vogel, H.J.3
-
179
-
-
0031165571
-
Optimization of electrostatic binding free energy
-
Lee L-P and Tidor B 1997 Optimization of electrostatic binding free energy J. Chem. Phys. 106 8681-90 (Pubitemid 127626875)
-
(1997)
Journal of Chemical Physics
, vol.106
, Issue.21
, pp. 8681-8690
-
-
Lee, L.-P.1
Tidor, B.2
-
180
-
-
21944443282
-
Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties
-
DOI 10.1063/1.477375, PII S0021960698505417
-
Kangas E and Tidor B 1998 Optimizing electrostatic affinity in ligand-receptor binding: theory, computation and ligand properties J. Chem. Phys. 109 7522-45 (Pubitemid 128674420)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.17
, pp. 7522-7545
-
-
Kangas, E.1
Tidor, B.2
-
181
-
-
73949142310
-
A 'reverse-Schur' approach to optimization with linear PDE constraints: Application to biomolecule analysis and design
-
10.1021/ct9001174 1549-9618
-
Bardhan J P, Altman M D, Tidor B and White J K 2009 A 'reverse-Schur' approach to optimization with linear PDE constraints: application to biomolecule analysis and design J. Chem. Theory Comput. 5 3260-78
-
(2009)
J. Chem. Theory Comput.
, vol.5
, Issue.12
, pp. 3260-3278
-
-
Bardhan, J.P.1
Altman, M.D.2
Tidor, B.3
White, J.K.4
-
182
-
-
0029489740
-
Application of the multiple reciprocity BEM to nonlinear potential problems
-
10.1016/0955-7997(95)00077-1 0955-7997
-
Nowak A J 1995 Application of the multiple reciprocity BEM to nonlinear potential problems Eng. Anal. Bound. Elem. 16 323-32
-
(1995)
Eng. Anal. Bound. Elem.
, vol.16
, Issue.4
, pp. 323-332
-
-
Nowak, A.J.1
-
183
-
-
0000542334
-
Development and parametrization of continuum solvent models. I. Models based on the boundary element method
-
Horvath D, vanBelle D, Lippens G and Wodak S J 1996 Development and parametrization of continuum solvent models. I Models based on the boundary element method J. Chem. Phys. 104 6679-95 (Pubitemid 126717302)
-
(1996)
Journal of Chemical Physics
, vol.104
, Issue.17
, pp. 6679-6695
-
-
Horvath, D.1
Van Belle, D.2
Lippens, G.3
Wodak, S.J.4
-
184
-
-
0042049850
-
Development and parametrization of continuum solvent models. II. A unified approach to the solvation problem
-
Horvath D, Lippens G and van Belle D 1996 Development and parametrization of continuum solvent models: II. A unified approach to the solvation problem J. Chem. Phys. 105 4197-210 (Pubitemid 126747486)
-
(1996)
Journal of Chemical Physics
, vol.105
, Issue.10
, pp. 4197-4210
-
-
Horvath, D.1
Lippens, G.2
Van Belle, D.3
-
185
-
-
84962346071
-
Dielectric Relaxation in Proteins: A Continuum Electrostatics Model Incorporating Dielectric Heterogeneity of the Protein and Time-Dependent Charges
-
DOI 10.1002/1096-987X(200102)22:3<290::AID-JCC1002>3.0.CO;2-V
-
Höfinger S and Simonson T 2001 Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges J. Comput. Chem. 22 290-305 (Pubitemid 33645659)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.3
, pp. 290-305
-
-
Hofinger, S.1
Simonson, T.2
-
186
-
-
0035894462
-
Making use of Connolly's molecular surface program in the isodensity adapted polarizable continuum model
-
DOI 10.1063/1.1421365
-
Höfinger S and Steinhauser O 2001 Making use of Connolly's molecular surface program in the isodensity adapted polarizable continuum model J. Chem. Phys. 115 10636-46 (Pubitemid 34063666)
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.23
, pp. 10636-10646
-
-
Hofinger, S.1
Steinhauser, O.2
-
187
-
-
84962408488
-
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
-
10.1016/j.cpc.2011.02.013 0010-4655
-
Yokota R, Bardhan J P, Knepley M G, Barba L A and Hamada T 2011 Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns Comput. Phys. Commun. 182 1272-83
-
(2011)
Comput. Phys. Commun.
, vol.182
, Issue.6
, pp. 1272-1283
-
-
Yokota, R.1
Bardhan, J.P.2
Knepley, M.G.3
Barba, L.A.4
Hamada, T.5
-
188
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y 0006-3525
-
Sanner M, Olson A J and Spehner J C 1996 Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 305-20
-
(1996)
Biopolymers
, vol.38
, Issue.3
, pp. 305-320
-
-
Sanner, M.1
Olson, A.J.2
Spehner, J.C.3
-
189
-
-
78651363914
-
TMSmesh: A robust method for molecular surface mesh generation using a trace technique
-
10.1021/ct100376g 1549-9618
-
Chen M and Lu B 2011 TMSmesh: a robust method for molecular surface mesh generation using a trace technique J. Chem. Theory Comput. 7 203-12
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.1
, pp. 203-212
-
-
Chen, M.1
Lu, B.2
-
190
-
-
84986465557
-
Computing the electric-potential of biomolecules: Application of a new method of molecular-surface triangulation
-
10.1002/jcc.540110509 0192-8651
-
Zauhar R J and Morgan R S 1990 Computing the electric-potential of biomolecules: application of a new method of molecular-surface triangulation J. Comput. Chem. 11 603-22
-
(1990)
J. Comput. Chem.
, vol.11
, Issue.5
, pp. 603-622
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
195
-
-
84961977361
-
Boundary element methods for dielectric cavity construction and integration
-
10.1063/1.1615232 0021-9606
-
Chen F W and Chipman D M 2003 Boundary element methods for dielectric cavity construction and integration J. Chem. Phys. 119 10289-97
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.19
, pp. 10289-10297
-
-
Chen, F.W.1
Chipman, D.M.2
-
196
-
-
0037375002
-
Dynamic maintenance and visualization of molecular surfaces
-
10.1016/S0166-218X(02)00283-4 0166-218X
-
Bajaj C L, Pascucci V, Shamir A, Holt R J and Netravali A N 2003 Dynamic maintenance and visualization of molecular surfaces Discrete Appl. Math. 127 23-51
-
(2003)
Discrete Appl. Math.
, vol.127
, Issue.1
, pp. 23-51
-
-
Bajaj, C.L.1
Pascucci, V.2
Shamir, A.3
Holt, R.J.4
Netravali, A.N.5
-
197
-
-
0032059253
-
A flexible triangulation method to describe the solvent-accessible surface of biopolymers
-
Juffer A H and Vogel P J 1998 A flexible triangulation method to describe the solvent-accessible surface of biopolymers J. Comput. - Aided Mol. Des. 12 289-99 (Pubitemid 128510957)
-
(1998)
Journal of Computer-Aided Molecular Design
, vol.12
, Issue.3
, pp. 289-299
-
-
Juffer, A.H.1
Vogel, H.J.2
-
198
-
-
84961983475
-
Molecular surface generation using marching tetrahedra
-
Chan S L and Purisima E O 1998 Molecular surface generation using marching tetrahedra J. Comput. Chem. 19 1268-77 (Pubitemid 128616669)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.11
, pp. 1268-1277
-
-
Chan, S.L.1
Purisima, E.O.2
-
200
-
-
0036434222
-
Molecular surface modeling and meshing
-
DOI 10.1007/s003660200018
-
Laug P and Borouchaki H 2002 Molecular surface modeling and meshing Eng. Comput. 18 199-210 (Pubitemid 35359461)
-
(2002)
Engineering with Computers
, vol.18
, Issue.3
, pp. 199-210
-
-
Laug, P.1
Borouchaki, H.2
-
201
-
-
33745587012
-
Quality meshing of implicit solvation models of biomolecular structures
-
DOI 10.1016/j.cagd.2006.01.008, PII S0167839606000215
-
Zhang Y, Xu G and Bajaj C 2006 Quality meshing of implicit solvation models of biomolecular structures Comput. Aided Geom. Des. 23 510-30 (Pubitemid 43993827)
-
(2006)
Computer Aided Geometric Design
, vol.23
, Issue.6
, pp. 510-530
-
-
Zhang, Y.1
Xu, G.2
Bajaj, C.3
-
203
-
-
84962401972
-
Analytical molecular surface calculation
-
10.1107/S0021889883010985 0021-8898
-
Connolly M L 1983 Analytical molecular surface calculation J. Appl. Cryst. 16 548-58
-
(1983)
J. Appl. Cryst.
, vol.16
, Issue.5
, pp. 548-558
-
-
Connolly, M.L.1
-
204
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic-acids
-
10.1126/science.6879170 0036-8075
-
Connolly M L 1983 Solvent-accessible surfaces of proteins and nucleic-acids Science 221 709-13
-
(1983)
Science
, vol.221
, Issue.4612
, pp. 709-713
-
-
Connolly, M.L.1
-
205
-
-
84961981991
-
A new definition of cavities for the computation of solvation free energies by the polarizable continuum model
-
Barone V, Cossi M and Tomasi J 1997 A new definition of cavities for the computation of solvation free energies by the polarizable continuum model J. Chem. Phys. 107 3210-21 (Pubitemid 127568937)
-
(1997)
Journal of Chemical Physics
, vol.107
, Issue.8
, pp. 3210-3221
-
-
Barone, V.1
Cossi, M.2
Tomasi, J.3
-
206
-
-
38349095051
-
Minimal molecular surfaces and their applications
-
10.1002/jcc.20796 0192-8651
-
Bates P W, Wei G W and Zhao S 2008 Minimal molecular surfaces and their applications J. Comput. Chem. 29 380-91
-
(2008)
J. Comput. Chem.
, vol.29
, Issue.3
, pp. 380-391
-
-
Bates, P.W.1
Wei, G.W.2
Zhao, S.3
-
207
-
-
0029968922
-
The contour-buildup algorithm to calculate the analytical molecular surface
-
DOI 10.1006/jsbi.1996.0022
-
Totrov M and Abagyan R 1996 The contour-buildup algorithm to calculate the analytical molecular surface J. Struct. Biol. 116 138-43 (Pubitemid 26093135)
-
(1996)
Journal of Structural Biology
, vol.116
, Issue.1
, pp. 138-143
-
-
Totrov, M.1
Abagyan, R.2
-
208
-
-
0037197254
-
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
-
DOI 10.1002/jcc.10061
-
Tsodikov O V, Record M T Jr and Sergeev Y V 2002 Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature J. Comput. Chem. 23 600-9 (Pubitemid 34312083)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.6
, pp. 600-609
-
-
Tsodikov, O.V.1
Thomas Record Jr., M.2
Sergeev, Y.V.3
-
209
-
-
30344480798
-
Molecular surface generation using a variable-radius solvent probe
-
DOI 10.1002/prot.20682
-
Bhat S and Purisima E O 2006 Molecular surface generation using a variable-radius solvent probe Proteins 62 244-61 (Pubitemid 43063022)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.62
, Issue.1
, pp. 244-261
-
-
Bhat, S.1
Purisima, E.O.2
-
210
-
-
0002441330
-
Triangulating the surface of a molecule
-
PII S0166218X96000546
-
Akkiraju N and Edelsbrunner H 1996 Triangulating the surface of a molecule Discrete Appl. Math. 71 5-22 (Pubitemid 126391769)
-
(1996)
Discrete Applied Mathematics
, vol.71
, Issue.1-3
, pp. 5-22
-
-
Akkiraju, N.1
Edelsbrunner, H.2
-
211
-
-
0032190305
-
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
-
DOI 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O
-
Liang J, Edelsbrunner H, Fu P, Sudhakar P V and Subramaniam S 1998 Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape Proteins 33 1-17 (Pubitemid 28413009)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.33
, Issue.1
, pp. 1-17
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
212
-
-
0032189626
-
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
-
DOI 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H
-
Liang J, Edelsbrunner H, Fu P, Sudhakar P V and Subramaniam S 1998 Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins Proteins 33 18-29 (Pubitemid 28413010)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.33
, Issue.1
, pp. 18-29
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
213
-
-
0033482642
-
Deformable smooth surface design
-
10.1007/PL00009412 0179-5376
-
Edelsbrunner H 1999 Deformable smooth surface design Discrete Comput. Geom. 21 87-115
-
(1999)
Discrete Comput. Geom.
, vol.21
, Issue.1
, pp. 87-115
-
-
Edelsbrunner, H.1
-
215
-
-
84867950208
-
Quality mesh generation for molecular skin surfaces using restricted union of balls
-
10.1016/j.comgeo.2008.10.001 0925-7721
-
Cheng H-L and Shi X 2009 Quality mesh generation for molecular skin surfaces using restricted union of balls Comput. Geom. 42 196-206
-
(2009)
Comput. Geom.
, vol.42
, Issue.3
, pp. 196-206
-
-
Cheng, H.-L.1
Shi, X.2
-
216
-
-
79958137314
-
Adaptive skin meshes coarsening for biomolecular simulation
-
10.1016/j.cagd.2011.04.001 0167-8396
-
Shi X and Koehl P 2011 Adaptive skin meshes coarsening for biomolecular simulation Comput. Aided Geom. Des. 28 307-20
-
(2011)
Comput. Aided Geom. Des.
, vol.28
, Issue.5
, pp. 307-320
-
-
Shi, X.1
Koehl, P.2
-
217
-
-
34548772137
-
Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations
-
10.1021/ct700001x 1549-9618
-
Lu B and McCammon J A 2007 Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations J. Chem. Theory Comput. 3 1134-42
-
(2007)
J. Chem. Theory Comput.
, vol.3
, Issue.3
, pp. 1134-1142
-
-
Lu, B.1
McCammon, J.A.2
-
218
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
10.1146/annurev.bb.06.060177.001055 0084-6589
-
Richards F M 1977 Areas, volumes, packing and protein structure Annu. Rev. Biophys. Bioeng. 6 151-76
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, Issue.1
, pp. 151-176
-
-
Richards, F.M.1
-
219
-
-
84962401972
-
Analytical molecular surface calculation
-
10.1107/S0021889883010985 0021-8898
-
Connolly M L 1983 Analytical molecular surface calculation J. Appl. Crystallogr. 16 548-58
-
(1983)
J. Appl. Crystallogr.
, vol.16
, Issue.5
, pp. 548-558
-
-
Connolly, M.L.1
-
222
-
-
34547842573
-
Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces
-
DOI 10.1063/1.2743423
-
Bardhan J P, Altman M D, White J K and Tidor B 2007 Numerical integration techniques for curved-panel discretizations of molecule-solvent interfaces J. Chem. Phys. 127 014701 (Pubitemid 47245139)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.1
, pp. 014701
-
-
Bardhan, J.P.1
Altman, M.D.2
Willis, D.J.3
Lippow, S.M.4
Tidor, B.5
White, J.K.6
-
223
-
-
84880765336
-
NETGEN - An advancing front 2D/3D-mesh generator based on abstract rules
-
Schöberl J 1997 NETGEN - An advancing front 2D/3D-mesh generator based on abstract rules Comput. Vis. Sci. 1 42-52
-
(1997)
Comput. Vis. Sci.
, vol.1
, pp. 42-52
-
-
Schöberl, J.1
-
224
-
-
77958035118
-
Fast molecular solvation energetics and forces computation
-
10.1137/090746173 1064-8275
-
Bajaj C and Zhao W 2010 Fast molecular solvation energetics and forces computation SIAM J. Sci. Comput. 31 4524-52
-
(2010)
SIAM J. Sci. Comput.
, vol.31
, Issue.6
, pp. 4524-4552
-
-
Bajaj, C.1
Zhao, W.2
-
225
-
-
79957592213
-
An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
-
10.1137/090764645 1064-8275
-
Bajaj C 2011 An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics SIAM J. Sci. Comput. 33 826-48
-
(2011)
SIAM J. Sci. Comput.
, vol.33
, Issue.2
, pp. 826-848
-
-
Bajaj, C.1
-
226
-
-
43149116830
-
A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics
-
Kuo S, Tidor B and White J 2008 A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics ACM J. Emerging Technol. Comput. Syst. 4 6
-
(2008)
ACM J. Emerging Technol. Comput. Syst.
, vol.4
, pp. 6
-
-
Kuo, S.1
Tidor, B.2
White, J.3
-
227
-
-
2342454337
-
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
-
10.1002/jcc.20000 0192-8651
-
Boschitsch A H and Fenley M O 2004 Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation J. Comput. Chem. 25 935-55
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.7
, pp. 935-955
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
228
-
-
84966247121
-
On the coupling of boundary integral and finite element methods
-
10.1090/S0025-5718-1980-0583487-9 0025-5718
-
Johnson C and Nedelec J C 1980 On the coupling of boundary integral and finite element methods Math. Comput. 35 1063-79
-
(1980)
Math. Comput.
, vol.35
, Issue.152
, pp. 1063-1079
-
-
Johnson, C.1
Nedelec, J.C.2
-
229
-
-
0001429464
-
Dielectric solvation dynamics of molecules of arbitrary shape and charge distribution
-
10.1063/1.475644 0021-9606
-
Song X and Chandler D 1998 Dielectric solvation dynamics of molecules of arbitrary shape and charge distribution J. Chem. Phys. 108 2594-8
-
(1998)
J. Chem. Phys.
, vol.108
, Issue.6
, pp. 2594-2598
-
-
Song, X.1
Chandler, D.2
-
230
-
-
62749167980
-
MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling
-
Song Y, Mao J and Gunner M R 2009 MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling J. Comput. Chem. 30 2231-47
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2231-2247
-
-
Song, Y.1
Mao, J.2
Gunner, M.R.3
-
231
-
-
0000486193
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: I. Algorithms and examples
-
10.1002/1096-987X(20001130)21:15<1319::AID-JCC1>3.0.CO;2-8 0192-8651
-
Holst M, Baker N and Wang F 2000 Adaptive multilevel finite element solution of the Poisson-Boltzmann equation: I. Algorithms and examples J. Comput. Chem. 21 1319-42
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.15
, pp. 1319-1342
-
-
Holst, M.1
Baker, N.2
Wang, F.3
-
232
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
DOI 10.1093/nar/gkh381
-
Dolinsky T J, Nielsen J E, McCammon J A and Baker N A 2004 PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 32 W665-7 (Pubitemid 38997419)
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
234
-
-
34548082000
-
Dipolar Poisson-Boltzmann equation: Ions and dipoles close to charge interfaces
-
DOI 10.1103/PhysRevLett.99.077801
-
Abrashkin A, Andelman D and Orland H 2007 Dipolar Poisson-Boltzmann equation: ions and dipoles close to charge interfaces Phys. Rev. Lett. 99 077801 (Pubitemid 47294621)
-
(2007)
Physical Review Letters
, vol.99
, Issue.7
, pp. 077801
-
-
Abrashkin, A.1
Andelman, D.2
Orland, H.3
-
235
-
-
58749107160
-
Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics
-
10.1529/biophysj.108.131649 0006-3495
-
Azuara C, Orland H, Bon M, Koehl P and Delarue M 2008 Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics Biophys. J. 95 5587-605
-
(2008)
Biophys. J.
, vol.95
, Issue.12
, pp. 5587-5605
-
-
Azuara, C.1
Orland, H.2
Bon, M.3
Koehl, P.4
Delarue, M.5
-
236
-
-
61549101824
-
Beyond the Poisson-Boltzmann: Modeling biomolecule-water and water-water interactions
-
10.1103/PhysRevLett.102.087801 0031-9007 087801
-
Koehl P, Orland H and Delarue M 2009 Beyond the Poisson-Boltzmann: modeling biomolecule-water and water-water interactions Phys. Rev. Lett. 102 087801
-
(2009)
Phys. Rev. Lett.
, vol.102
, Issue.8
-
-
Koehl, P.1
Orland, H.2
Delarue, M.3
-
237
-
-
66349114495
-
Computing ion solvation free energies using the dipolar Poisson model
-
10.1021/jp9010907 1520-6106 B
-
Koehl P, Orland H and Delarue M 2009 Computing ion solvation free energies using the dipolar Poisson model J. Phys. Chem. B 113 5694-7
-
(2009)
J. Phys. Chem.
, vol.113
, Issue.17
, pp. 5694-5697
-
-
Koehl, P.1
Orland, H.2
Delarue, M.3
-
238
-
-
14244273182
-
Theory and applications of the Generalized Born solvation model in macromolecular simulations
-
DOI 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
-
Tsui V and Case D A 2001 Theory and applications of the generalized Born solvation model in macromolecular simulations Biopolymers 56 275-91 (Pubitemid 34105875)
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
239
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
10.1016/j.sbi.2008.01.003 0959-440X
-
Chen J, Brooks C L III and Khandogin J 2008 Recent advances in implicit solvent-based methods for biomolecular simulations Curr. Opin. Struc. Biol. 18 140-8
-
(2008)
Curr. Opin. Struc. Biol.
, vol.18
, Issue.2
, pp. 140-148
-
-
Chen, J.1
Brooks, C.L.2
Khandogin, J.3
-
241
-
-
0025661993
-
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
-
10.1016/S0022-2836(99)80019-9 0022-2836
-
Schaefer M and Froemmel C 1990 A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution J. Mol. Biol. 216 1045-66
-
(1990)
J. Mol. Biol.
, vol.216
, Issue.4
, pp. 1045-1066
-
-
Schaefer, M.1
Froemmel, C.2
-
242
-
-
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 1578-99 (Pubitemid 126789971)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.5
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
243
-
-
0031358503
-
Dielectric screening treatment of electrostatic solvation
-
Luo R, Moult J and Gilson M K 1997 Dielectric screening treatment of electrostatic solvation J. Phys. Chem. B 101 11226-36 (Pubitemid 127627979)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.51
, pp. 11226-11236
-
-
Luo, R.1
Moult, J.2
Gilson, M.K.3
-
244
-
-
0001246294
-
Generalized born model based on a surface integral formulation
-
Ghosh A, Rapp C S and Friesner R A 1998 Generalized Born model based on a surface integral formulation J. Phys. Chem. B 102 10983-90 (Pubitemid 128716615)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.52
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
245
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
-
10.1007/s002140050460 1432-881X
-
Srinivasan J, Trevathan M W, Beroza P and Case D A 1999 Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects Theor. Chem. Acc. 101 426-34
-
(1999)
Theor. Chem. Acc.
, vol.101
, Issue.6
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
246
-
-
80053497850
-
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
-
10.1063/1.3641485 0021-9606 124107
-
Bardhan J P and Knepley M G 2011 Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions J. Chem. Phys. 135 124107
-
(2011)
J. Chem. Phys.
, vol.135
, Issue.12
-
-
Bardhan, J.P.1
Knepley, M.G.2
-
247
-
-
54949135400
-
Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory
-
10.1063/1.2987409 0021-9606 144105
-
Bardhan J P 2008 Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory J. Chem. Phys. 129 144105
-
(2008)
J. Chem. Phys.
, vol.129
, Issue.14
-
-
Bardhan, J.P.1
-
248
-
-
22944441922
-
Incorporating variable dielectric environments into the generalized Born model
-
DOI 10.1063/1.1857811, 094511
-
Sigalov G, Scheffel P and Onufriev A 2005 Incorporating variable dielectric environments into the generalized Born model J. Chem. Phys. 122 094511 (Pubitemid 41042160)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.9
, pp. 1-15
-
-
Sigalov, G.1
Scheffel, P.2
Onufriev, A.3
-
250
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
10.1016/0009-2614(95)01082-K 0009-2614
-
Hawkins G D, Cramer C J and Truhlar D G 1995 Pairwise solute descreening of solute charges from a dielectric medium Chem. Phys. Lett. 246 122-9
-
(1995)
Chem. Phys. Lett.
, vol.246
, Issue.1-2
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
251
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
10.1021/ja00172a038 0002-7863
-
Still W C, Tempczyk A, Hawley R C and Hendrickson T F 1990 Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 112 6127-9
-
(1990)
J. Am. Chem. Soc.
, vol.112
, Issue.16
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.F.4
-
252
-
-
0038792211
-
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
-
10.1002/jcc.10272 0192-8651
-
Lee M S, Feig M, Salsbury F R and Brooks C L III 2003 New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations J. Comput. Chem. 24 1348-56
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.11
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.3
Brooks, C.L.4
-
253
-
-
0141453063
-
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
-
10.1063/1.1595641 0021-9606
-
Grycuk T 2003 Deficiency of the Coulomb-field approximation in the generalized Born model: an improved formula for Born radii evaluation J. Chem. Phys. 119 4817-26
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.9
, pp. 4817-4826
-
-
Grycuk, T.1
-
254
-
-
10044243843
-
Generalized Born model: Analysis, refinement and applications to proteins
-
10.1021/jp046748b 1520-6106 B
-
Wojciechowski M and Lesyng B 2004 Generalized Born model: analysis, refinement and applications to proteins J. Phys. Chem. B 108 18368-76
-
(2004)
J. Phys. Chem.
, vol.108
, Issue.47
, pp. 18368-18376
-
-
Wojciechowski, M.1
Lesyng, B.2
-
255
-
-
8344229165
-
Surface generalized Born method: A simple, fast and precise implicit solvent model beyond the Coulomb approximation
-
10.1021/jp046721s 1089-5639 A
-
Romanov A N, Jabin S N, Martynov Y B, Sulimov A V, Grigoriev F V and Sulimov V B 2004 Surface generalized Born method: a simple, fast and precise implicit solvent model beyond the Coulomb approximation J. Phys. Chem. A 108 9323-7
-
(2004)
J. Phys. Chem.
, vol.108
, Issue.43
, pp. 9323-9327
-
-
Romanov, A.N.1
Jabin, S.N.2
Martynov, Y.B.3
Sulimov, A.V.4
Grigoriev, F.V.5
Sulimov, V.B.6
-
256
-
-
0000747830
-
A Gaussian description of molecular shape
-
10.1021/j100011a016 0022-3654
-
Grant J A and Pickup B T 1995 A Gaussian description of molecular shape J. Phys. Chem. 99 3503-10
-
(1995)
J. Phys. Chem.
, vol.99
, Issue.11
, pp. 3503-3510
-
-
Grant, J.A.1
Pickup, B.T.2
-
257
-
-
34249109453
-
G Br6 NL: A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation
-
DOI 10.1063/1.2735322
-
6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation J. Chem. Phys. 126 195102 (Pubitemid 46794153)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.19
, pp. 195102
-
-
Tjong, H.1
Zhou, H.-X.2
-
258
-
-
0042880954
-
Computing the electrostatic free-energy of complex molecules: The variational Coulomb field approximation
-
10.1063/1.1589745 0021-9606
-
Borgis D, Lévy N and Marchi M 2003 Computing the electrostatic free-energy of complex molecules: the variational Coulomb field approximation J. Chem. Phys. 119 3516-28
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.6
, pp. 3516-3528
-
-
Borgis, D.1
Lévy, N.2
Marchi, M.3
-
259
-
-
0035156429
-
Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome
-
10.1002/1097-0282(200101)58:1<106::AID-BIP100>3.0.CO;2-# 0006-3525
-
Beard D A and Schlick T 2001 Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome Biopolymers 58 106-15
-
(2001)
Biopolymers
, vol.58
, Issue.1
, pp. 106-115
-
-
Beard, D.A.1
Schlick, T.2
-
260
-
-
0017389770
-
Interactions of highly charged colloidal cylinders with applications to double stranded DNA
-
Stigter D 1977 Interactions of highly charged colloidal cylinders with applications to double-stranded DNA Biopolymers 16 1435-48 (Pubitemid 8110411)
-
(1977)
Biopolymers
, vol.16
, Issue.7
, pp. 1435-1448
-
-
Stigter, D.1
-
261
-
-
33748501925
-
Effective charges for macromolecules in a solvent
-
10.1021/jp953109f 0022-3654
-
Gabdoulline R R and Wade R C 1996 Effective charges for macromolecules in a solvent J. Phys. Chem. 100 3868-78
-
(1996)
J. Phys. Chem.
, vol.100
, Issue.9
, pp. 3868-3878
-
-
Gabdoulline, R.R.1
Wade, R.C.2
-
262
-
-
62549159547
-
Bounding the electrostatic free energies associated with linear continuum models of molecular solvation
-
10.1063/1.3081148 0021-9606 104108
-
Bardhan J P, Knepley M G and Anitescu M 2009 Bounding the electrostatic free energies associated with linear continuum models of molecular solvation J. Chem. Phys. 130 104108
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.10
-
-
Bardhan, J.P.1
Knepley, M.G.2
Anitescu, M.3
-
263
-
-
0346971105
-
Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
10.1002/jcc.10378 0192-8651
-
Feig M, Onufriev A, Lee M S, Im W, Case D A and Brooks C L III 2004 Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 25 265-84
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.2
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
264
-
-
78650545454
-
PetFMM - A dynamically load-balancing parallel fast multipole library
-
10.1002/nme.2972 0029-5981
-
Cruz F A, Knepley M G and Barba L A 2011 PetFMM - a dynamically load-balancing parallel fast multipole library Int. J. Numer. Methods Eng. 85 403-28
-
(2011)
Int. J. Numer. Methods Eng.
, vol.85
, Issue.4
, pp. 403-428
-
-
Cruz, F.A.1
Knepley, M.G.2
Barba, L.A.3
-
265
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
10.1021/cr00023a004 0009-2665
-
Kollman P 1993 Free energy calculations: applications to chemical and biochemical phenomena Chem. Rev. 93 2395-417
-
(1993)
Chem. Rev.
, vol.93
, Issue.7
, pp. 2395-2417
-
-
Kollman, P.1
-
266
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina M, Beglov D and Roux B 1997 Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations J. Phys. Chem. B 101 5239-48 (Pubitemid 127609289)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.26
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
267
-
-
0032968444
-
Optimized atomic radii for protein continuum electrostatics solvation forces
-
DOI 10.1016/S0301-4622(98)00236-1, PII S0301462298002361
-
Nina M, Im W and Roux B 1999 Optimized atomic radii for protein continuum electrostatics solvation forces Biophys. Chem. 78 89-96 (Pubitemid 29206659)
-
(1999)
Biophysical Chemistry
, vol.78
, Issue.1-2
, pp. 89-96
-
-
Nina, M.1
Im, W.2
Roux, B.3
-
268
-
-
0037168282
-
Atomic radii for continuum electrostatics calculations on nucleic acids
-
DOI 10.1021/jp025852v
-
Banavali N K and Roux B 2002 Atomic radii for continuum electrostatics calculations on nucleic acids J. Phys. Chem. B 106 11026-35 (Pubitemid 35410240)
-
(2002)
Journal of Physical Chemistry B
, vol.106
, Issue.42
, pp. 11026-11035
-
-
Banavali, N.K.1
Roux, B.2
-
269
-
-
23844475490
-
Optimized radii for Poisson-Boltzmann calculations with the AMBER force field
-
10.1021/ct049834o 1549-9618
-
Swanson J M J, Adcock S A and McCammon J A 2005 Optimized radii for Poisson-Boltzmann calculations with the AMBER force field J. Chem. Theory Comput. 1 484-93
-
(2005)
J. Chem. Theory Comput.
, vol.1
, Issue.3
, pp. 484-493
-
-
Swanson, J.M.J.1
Adcock, S.A.2
McCammon, J.A.3
-
270
-
-
45549096845
-
Optimized parameters for continuum solvation calculations with carbohydrates
-
10.1021/jp709725b 1520-6106 B
-
Green D F 2008 Optimized parameters for continuum solvation calculations with carbohydrates J. Phys. Chem. B 112 5238-49
-
(2008)
J. Phys. Chem.
, vol.112
, Issue.16
, pp. 5238-5249
-
-
Green, D.F.1
-
271
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field
-
10.1021/ja057216r 0002-7863
-
Chen J, Im W and Brooks C L III 2006 Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field J. Am. Chem. Soc. 128 3728-36
-
(2006)
J. Am. Chem. Soc.
, vol.128
, Issue.11
, pp. 3728-3736
-
-
Chen, J.1
Im, W.2
Brooks, C.L.3
-
272
-
-
11744353229
-
The computation of a potential of mean force: Choice of the biasing potential in the umbrella sampling technique
-
10.1063/1.466628 0021-9606
-
Beutler T C and van Gunsteren W F 1993 The computation of a potential of mean force: choice of the biasing potential in the umbrella sampling technique J. Chem. Phys. 100 1492-7
-
(1993)
J. Chem. Phys.
, vol.100
, Issue.2
, pp. 1492-1497
-
-
Beutler, T.C.1
Van Gunsteren, W.F.2
-
273
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
-
10.1063/1.1739396 0021-9606
-
Izvekov S, Parrinello M, Burnham C J and Voth G A 2004 Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching J. Chem. Phys. 120 10896-913
-
(2004)
J. Chem. Phys.
, vol.120
, Issue.23
, pp. 10896-10913
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
274
-
-
34147116967
-
Automated parameterization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching
-
10.1021/ct600284f 1549-9618
-
Maurer P, Laio A, Hugosson H W, Colombo M C and Rothlisberger U 2007 Automated parameterization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching J. Chem. Theory Comput. 3 628-39
-
(2007)
J. Chem. Theory Comput.
, vol.3
, Issue.2
, pp. 628-639
-
-
Maurer, P.1
Laio, A.2
Hugosson, H.W.3
Colombo, M.C.4
Rothlisberger, U.5
-
275
-
-
0001348705
-
Parameter dependence in continuum electrostatic calculations: A study using protein salt bridges
-
Hendsch Z S, Sindelar C V and Tidor B 1998 Parameter dependence on continuum electrostatic calculations: a study using protein salt bridges J. Phys. Chem. B 102 4404-10 (Pubitemid 128576715)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.22
, pp. 4404-4410
-
-
Hendsch, Z.S.1
Sindelar, C.V.2
Tidor, B.3
-
276
-
-
0001342592
-
Comment on the validation of continuum electrostatics models
-
Scarsi M and Caflisch A 1999 Comment on the validation of continuum electrostatics models J. Comput. Chem. 20 1533-6 (Pubitemid 129651767)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.14
, pp. 1533-1536
-
-
Scarsi, M.1
Caflisch, A.2
-
277
-
-
0037693081
-
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations
-
10.1002/jcc.10261 0192-8651
-
Rankin K N, Sulea T and Purisima E O 2003 On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations J. Comput. Chem. 24 954-62
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.8
, pp. 954-962
-
-
Rankin, K.N.1
Sulea, T.2
Purisima, E.O.3
-
278
-
-
5444263980
-
The parameterization and validation of generalized Born models using the pairwise descreening approximation
-
10.1002/jcc.20105 0192-8651
-
Michel J, Taylor R D and Essex J W 2004 The parameterization and validation of generalized Born models using the pairwise descreening approximation J. Comput. Chem. 25 1760-70
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.14
, pp. 1760-1770
-
-
Michel, J.1
Taylor, R.D.2
Essex, J.W.3
-
279
-
-
0000705154
-
Parametrizing a polarizable force field from ab initio data: I. The fluctuating point charge model
-
10.1063/1.478043 0021-9606
-
Banks J L, Kaminski G A, Zhou R H, Mainz D T, Berne B J and Friesner R A 1999 Parametrizing a polarizable force field from ab initio data: I. The fluctuating point charge model J. Chem. Phys. 110 741-54
-
(1999)
J. Chem. Phys.
, vol.110
, Issue.2
, pp. 741-754
-
-
Banks, J.L.1
Kaminski, G.A.2
Zhou, R.H.3
Mainz, D.T.4
Berne, B.J.5
Friesner, R.A.6
-
281
-
-
36749024620
-
Polarizable force fields: History, test cases and prospects
-
10.1021/ct700127w 1549-9618
-
Warshel A, Kato M and Pisliakov A V 2007 Polarizable force fields: history, test cases and prospects J. Chem. Theory Comput. 3 2034-45
-
(2007)
J. Chem. Theory Comput.
, vol.3
, Issue.6
, pp. 2034-2045
-
-
Warshel, A.1
Kato, M.2
Pisliakov, A.V.3
-
282
-
-
77749298172
-
Current status of the AMOEBA polarizable force field
-
10.1021/jp910674d 1520-6106 B
-
Ponder J W et al 2010 Current status of the AMOEBA polarizable force field J. Phys. Chem. B 114 2549-64
-
(2010)
J. Phys. Chem.
, vol.114
, Issue.8
, pp. 2549-2564
-
-
Ponder, J.W.1
-
283
-
-
1642357706
-
The Many Roles of Computation in Drug Discovery
-
DOI 10.1126/science.1096361
-
Jorgensen W L 2004 The many roles of computation in drug discovery Science 303 1813-8 (Pubitemid 38374866)
-
(2004)
Science
, vol.303
, Issue.5665
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
284
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
Jorgensen W L, Maxwell D S and Tirado-Rives J 1996 Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 11225-36 (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
285
-
-
2942532422
-
Development and testing of a general AMBER force field
-
10.1002/jcc.20035 0192-8651
-
Wang J, Wolf R M, Caldwell J W, Kollman P A and Case D A 2004 Development and testing of a general AMBER force field J. Comput. Chem. 25 1157-74
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.9
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
286
-
-
79951997463
-
A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets
-
10.1002/jcc.21671 0192-8651
-
Mukherjee G, Patra N, Barua P and Jayaram B 2011 A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets J. Comput. Chem. 32 893-907
-
(2011)
J. Comput. Chem.
, vol.32
, Issue.5
, pp. 893-907
-
-
Mukherjee, G.1
Patra, N.2
Barua, P.3
Jayaram, B.4
-
287
-
-
76249087938
-
CHARMM general force field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
-
Vanommeslaeghe K et al 2010 CHARMM general force field (CGenFF): a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 31 671-90
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
-
288
-
-
0001458825
-
The aqueous solvation of water: A comparison of continuum methods with molecular dynamics
-
Rick S W and Berne B J 1994 The aqueous solvation of water: a comparison of continuum methods with molecular dynamics J. Am. Chem. Soc. 116 3949-54 (Pubitemid 24980982)
-
(1994)
Journal of the American Chemical Society
, vol.116
, Issue.9
, pp. 3949-3954
-
-
Rick, S.W.1
Berne, B.J.2
-
289
-
-
85022423714
-
Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations
-
10.1021/ja00004a079 0002-7863
-
Jean-Charles A, Nicholls A, Sharp K, Honig B, Tempczyk A, Hendrickson T F and Still W C 1991 Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations J. Am. Chem. Soc. 113 1454-5
-
(1991)
J. Am. Chem. Soc.
, vol.113
, Issue.4
, pp. 1454-1455
-
-
Jean-Charles, A.1
Nicholls, A.2
Sharp, K.3
Honig, B.4
Tempczyk, A.5
Hendrickson, T.F.6
Still, W.C.7
-
290
-
-
33748640631
-
Calculation of alkane to water solvation free energies using continuum solvent models
-
Sitkoff D, BenTal N and Honig B 1996 Calculation of alkane to water solvation free energies using continuum solvent models J. Phys. Chem. 100 2744-52 (Pubitemid 126793230)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.7
, pp. 2744-2752
-
-
Sitkoff, D.1
Ben-Tal, N.2
Honig, B.3
-
291
-
-
0036286851
-
Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
-
10.1021/ar0100273 0001-4842
-
Makarov V, Pettitt B M and Feig M 2002 Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment Acc. Chem. Res. 35 376-84
-
(2002)
Acc. Chem. Res.
, vol.35
, Issue.6
, pp. 376-384
-
-
Makarov, V.1
Pettitt, B.M.2
Feig, M.3
-
292
-
-
0000760120
-
A failure of continuum theory: Temperature dependence of the solvent reorganization energy of electron transfer in highly polar solvents
-
10.1021/jp990494q 1520-6106 B
-
Vath P, Zimmt M B, Matyushov D V and Voth G A 1999 A failure of continuum theory: temperature dependence of the solvent reorganization energy of electron transfer in highly polar solvents J. Phys. Chem. B 103 9130-40
-
(1999)
J. Phys. Chem.
, vol.103
, Issue.43
, pp. 9130-9140
-
-
Vath, P.1
Zimmt, M.B.2
Matyushov, D.V.3
Voth, G.A.4
-
294
-
-
0001315749
-
A model of a local dielectric constant in proteins
-
10.1063/1.475602 0021-9606
-
Voges D and Karshikoff A 1998 A model of a local dielectric constant in proteins J. Chem. Phys. 108 2219-27
-
(1998)
J. Chem. Phys.
, vol.108
, Issue.5
, pp. 2219-2227
-
-
Voges, D.1
Karshikoff, A.2
-
295
-
-
79952731796
-
A theory for the anisotropic and inhomogeneous dielectric properties of proteins
-
10.1039/c0cp02061c 1463-9076
-
Guest W C, Cashman N R and Plotkin S S 2011 A theory for the anisotropic and inhomogeneous dielectric properties of proteins Phys. Chem. Chem. Phys. 13 6286-95
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, Issue.13
, pp. 6286-6295
-
-
Guest, W.C.1
Cashman, N.R.2
Plotkin, S.S.3
-
296
-
-
33748593093
-
as of ionizable groups in proteins
-
Demchuk E and Wade R C 1996 Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins J. Phys. Chem. 100 17373-87 (Pubitemid 126790125)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.43
, pp. 17373-17387
-
-
Demchuk, E.1
Wade, R.C.2
-
297
-
-
0031564641
-
Modeling of protein conformational fluctuations in pK(a) predictions
-
DOI 10.1006/jmbi.1997.0895
-
Zhou H-X and Vijayakumar M 1997 Modeling of protein conformational fluctuations in pKa predictions J. Mol. Biol. 267 1002-11 (Pubitemid 27192668)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.4
, pp. 1002-1011
-
-
Zhou, H.-X.1
Vijayakumar, M.2
-
298
-
-
0030945495
-
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
-
Alexov E G and Gunner M R 1997 Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties Biophys. J. 72 2075-93 (Pubitemid 27184435)
-
(1997)
Biophysical Journal
, vol.72
, Issue.5
, pp. 2075-2093
-
-
Alexov, E.G.1
Gunner, M.R.2
-
299
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins
-
10.1016/S0006-3495(02)73940-4 0006-3495
-
Georgescu R E, Alexov E G and Gunner M R 2002 Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins Biophys. J. 83 1731-48
-
(2002)
Biophys. J.
, vol.83
, Issue.4
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
300
-
-
0037305552
-
On the evaluation and optimization of protein X-ray structures for pKa calculations
-
DOI 10.1110/ps.0229903
-
Nielsen J E and McCammon J A 2003 On the evaluation and optimization of protein x-ray structures for pKa calculations Protein Sci. 12 313-26 (Pubitemid 36120344)
-
(2003)
Protein Science
, vol.12
, Issue.2
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
301
-
-
34250702227
-
Implications of a high dielectric constant in proteins
-
DOI 10.1063/1.2741543
-
Lund M, Jönsson B and Woodward C E 2007 Implications of a high dielectric constant in proteins J. Chem. Phys. 126 225103 (Pubitemid 46964792)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.22
, pp. 225103
-
-
Lund, M.1
Jonsson, B.2
Woodward, C.E.3
-
302
-
-
0028204490
-
Do salt bridges stabilize proteins? A continuum electrostatic analysis
-
Hendsch Z S and Tidor B 1994 Do salt bridges stabilize proteins? A continuum electrostatic analysis Protein Sci. 3 211-26 (Pubitemid 24086354)
-
(1994)
Protein Science
, vol.3
, Issue.2
, pp. 211-226
-
-
Hendsch, Z.S.1
Tidor, B.2
-
303
-
-
0035797737
-
Salt bridges stabilize the folded structure of barnase
-
DOI 10.1021/jp011214l
-
Vijayakumar M and Zhou H-X 2001 Salt bridges stabilize the folded structure of barnase J. Phys. Chem. B 105 7334-40 (Pubitemid 35338957)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.30
, pp. 7334-7340
-
-
Vijayakumar, M.1
Zhou, H.-X.2
-
304
-
-
0038650855
-
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
-
Dong F, Vijayakumar M and Zhou H-X 2003 Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar Biophys. J. 85 49-60 (Pubitemid 36753615)
-
(2003)
Biophysical Journal
, vol.85
, Issue.1
, pp. 49-60
-
-
Dong, F.1
Vijayakumar, M.2
Zhou, H.-X.3
-
305
-
-
4444301075
-
How optimal are the binding energetics of barnase and barstar?
-
DOI 10.1529/biophysj.104.040964
-
Wang T, Tomic S, Gabdoulline R R and Wade R C 2004 How optimal are the binding energetics of barnase and barstar? Biophys. J. 87 1618-30 (Pubitemid 39167019)
-
(2004)
Biophysical Journal
, vol.87
, Issue.3
, pp. 1618-1630
-
-
Wang, T.1
Tomic, S.2
Gabdoulline, R.R.3
Wade, R.C.4
-
306
-
-
0031276965
-
A stringent test of the cavity concept in continuum dielectrics
-
Papazyan A and Warshel A 1997 A stringent test of the cavity concept in continuum dielectrics J. Chem. Phys. 107 7975-8 (Pubitemid 127564325)
-
(1997)
Journal of Chemical Physics
, vol.107
, Issue.19
, pp. 7975-7978
-
-
Papazyan, A.1
Warshel, A.2
-
307
-
-
0001397317
-
Effect of solvent discreteness on solvation
-
Papazyan A and Warshel A 1998 Effect of solvent discreteness on solvation J. Phys. Chem. B 102 5348-57 (Pubitemid 128578373)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.27
, pp. 5348-5357
-
-
Papazyan, A.1
Warshel, A.2
-
308
-
-
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 11254-64 (Pubitemid 127627983)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.51
, pp. 11254-11264
-
-
Papazyan, A.1
Warshel, A.2
-
309
-
-
54849411174
-
On the dielectric boundary in Poisson-Boltzmann calculations
-
10.1021/ct700319x 1549-9618
-
Tjong H and Zhou H-X 2008 On the dielectric boundary in Poisson-Boltzmann calculations J. Chem. Theory Comput. 4 507-14
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.3
, pp. 507-514
-
-
Tjong, H.1
Zhou, H.-X.2
-
311
-
-
77956414486
-
Differential geometry based solvation model: I. Eulerian formulation
-
10.1016/j.jcp.2010.06.036 0021-9991
-
Chen Z, Baker N A and Wei G W 2010 Differential geometry based solvation model: I. Eulerian formulation J. Comput. Phys. 229 8231-58
-
(2010)
J. Comput. Phys.
, vol.229
, Issue.22
, pp. 8231-8258
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
312
-
-
33749603363
-
How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis
-
DOI 10.1021/jp063479b
-
Tan C, Yang L and Luo R 2006 How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis J. Phys. Chem. B 110 18680-7 (Pubitemid 44547378)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.37
, pp. 18680-18687
-
-
Tan, C.1
Yang, L.2
Luo, R.3
-
313
-
-
0042139644
-
Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease
-
10.1002/(SICI)1096-987X(200003)21:4<295::AID-JCC5>3.0.CO;2-8 0192-8651
-
David L, Luo R and Gilson M K 2000 Comparison of generalized Born and Poisson models: energetics and dynamics of HIV protease J. Comput. Chem. 21 295-309
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.4
, pp. 295-309
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
314
-
-
20644436466
-
Solvent models for protein-ligand binding: Comparison of implicit solvent Poisson and Surface Generalized Born models with explicit solvent simulations
-
DOI 10.1002/jcc.1031
-
Zhang L Y, Gallicchio E, Friesner R A and Levy R M 2001 Solvent models for protein-ligand binding: comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations J. Comput. Chem. 22 591-607 (Pubitemid 32382606)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.6
, pp. 591-607
-
-
Levy, R.M.1
-
315
-
-
0036234027
-
Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
-
DOI 10.1023/A:1014929925008
-
Xia B, Tsui V, Case D A, Dyson H J and Wright P E 2002 Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model and with explicit water J. Biomolecular NMR 22 317-31 (Pubitemid 34449944)
-
(2002)
Journal of Biomolecular NMR
, vol.22
, Issue.4
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, H.J.4
Wright, P.E.5
-
316
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
DOI 10.1073/pnas.2232868100
-
Nymeyer H and García A E 2003 Simulation of the folding equilibrium of helical peptides: a comparison of the generalized Born approximation with explicit solvent Proc. Natl Acad. Sci. USA 100 13934-9 (Pubitemid 37499169)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.SUPPL. 2
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
317
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
-
10.1073/pnas.142430099 0027-8424
-
Zhou R and Berne B J 2002 Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl Acad. Sci. USA 99 12777-82
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, Issue.20
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
-
318
-
-
2942700087
-
Comment on 'Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?' the Poisson-Boltzmann equation
-
10.1021/jp037812c 1520-6106 B
-
Zhou R, Krilov G and Berne B J 2004 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 7528-30
-
(2004)
J. Phys. Chem.
, vol.108
, Issue.22
, pp. 7528-7530
-
-
Zhou, R.1
Krilov, G.2
Berne, B.J.3
-
319
-
-
3442893249
-
Molecular dynamics simulations of DNA using the generalized Born solvation model: Quantitative comparisons with explicit solvation results
-
10.1021/jp048757q 1520-6106 B
-
Sands Z A and Laughton C A 2004 Molecular dynamics simulations of DNA using the generalized Born solvation model: quantitative comparisons with explicit solvation results J. Phys. Chem. B 108 10113-9
-
(2004)
J. Phys. Chem.
, vol.108
, Issue.28
, pp. 10113-10119
-
-
Sands, Z.A.1
Laughton, C.A.2
-
320
-
-
14544285906
-
Comparative study of generalized born models: Born radii and peptide folding
-
DOI 10.1021/jp046307s
-
Zhu J, Alexov E and Honig B 2005 Comparative study of generalized Born models: Born radii and peptide folding J. Phys. Chem. B 109 3008-22 (Pubitemid 40304482)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.7
, pp. 3008-3022
-
-
Zhu, J.1
Alexov, E.2
Honig, B.3
-
321
-
-
0034510764
-
Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models
-
DOI 10.1021/jp0027602
-
Bursulaya B D and Brooks C L III 2000 Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models J. Phys. Chem. B 104 12378-83 (Pubitemid 32087823)
-
(2000)
Journal of Physical Chemistry B
, vol.104
, Issue.51
, pp. 12378-12383
-
-
Bursulaya, B.D.1
Brooks III, C.L.2
-
322
-
-
0031075977
-
Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
-
Edinger S R, Cortis C, Shenkin P S and Friesner R A 1997 Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation J. Phys. Chem. B 101 1190-7 (Pubitemid 127591367)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.7
, pp. 1190-1197
-
-
Edinger, S.R.1
Cortis, C.2
Shenkin, P.S.3
Friesner, R.A.4
-
323
-
-
65249147164
-
Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model
-
10.1021/ct800445x 1549-9618
-
Shivakumar D, Deng Y and Roux B 2009 Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model J. Chem. Theory Comput. 5 919-30
-
(2009)
J. Chem. Theory Comput.
, vol.5
, Issue.4
, pp. 919-930
-
-
Shivakumar, D.1
Deng, Y.2
Roux, B.3
-
324
-
-
0036217783
-
Long time dynamics of Met-enkephalin: Comparison of explicit and implicit solvent models
-
Shen M and Freed K F 2002 Long time dynamics of Met-Enkephalin: comparison of explicit and implicit solvent models Biophys. J. 82 1791-808 (Pubitemid 34280796)
-
(2002)
Biophysical Journal
, vol.82
, Issue.4
, pp. 1791-1808
-
-
Shen, M.-Y.1
Freed, K.F.2
-
325
-
-
33847723384
-
Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
-
DOI 10.1021/jp066831u
-
Roe D R, Okur A, Wickstrom L, Hornak V and Simmerling C 2007 Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation J. Phys. Chem. B 111 1846-57 (Pubitemid 46384278)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.7
, pp. 1846-1857
-
-
Roe, D.R.1
Okur, A.2
Wickstrom, L.3
Hornak, V.4
Simmerling, C.5
-
326
-
-
33749637456
-
Free energy calculations of ion hydration: An analysis of the Born model in terms of microscopic simulations
-
10.1021/j100347a081 0022-3654
-
Jayaram B, Fine R, Sharp K and Honig B 1989 Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations J. Phys. Chem. 93 4320-7
-
(1989)
J. Phys. Chem.
, vol.93
, Issue.10
, pp. 4320-4327
-
-
Jayaram, B.1
Fine, R.2
Sharp, K.3
Honig, B.4
-
327
-
-
0030134110
-
On the validity of electrostatic linear response in polar solvents
-
Åqvist J and Hansson T 1996 On the validity of electrostatic linear response in polar solvents J. Phys. Chem. 100 9512-21 (Pubitemid 126834549)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.22
, pp. 9512-9521
-
-
Aqvist, J.1
Hansson, T.2
-
328
-
-
38449120033
-
Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
-
DOI 10.1063/1.2771171
-
Cerutti D S, Baker N A and McCammon J A 2007 Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? J. Chem. Phys. 127 155101 (Pubitemid 351260821)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.15
, pp. 155101
-
-
Cerutti, D.S.1
Baker, N.A.2
McCammon, J.A.3
-
329
-
-
79952001306
-
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water
-
10.1002/jcc.21668 0192-8651
-
Lin B and Pettitt B M 2010 Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water J. Comput. Chem. 32 878-85
-
(2010)
J. Comput. Chem.
, vol.32
, Issue.5
, pp. 878-885
-
-
Lin, B.1
Pettitt, B.M.2
-
330
-
-
80052415405
-
Electric field inside a 'Rossky cavity' in uniformly polarized water
-
10.1063/1.3628679 0021-9606 084514
-
Martin D R, Friesen A D and Matyushov D V 2011 Electric field inside a 'Rossky cavity' in uniformly polarized water J. Chem. Phys. 135 084514
-
(2011)
J. Chem. Phys.
, vol.135
, Issue.8
-
-
Martin, D.R.1
Friesen, A.D.2
Matyushov, D.V.3
-
331
-
-
0000381797
-
Surface of active polarons: A semiexplicit method for biomolecular dynamics
-
10.1063/1.481364 0021-9606
-
Kimura S R, Brower R C, Zhang C and Sugimori M 2000 Surface of active polarons: a semiexplicit method for biomolecular dynamics J. Chem. Phys. 112 7723-34
-
(2000)
J. Chem. Phys.
, vol.112
, Issue.17
, pp. 7723-7734
-
-
Kimura, S.R.1
Brower, R.C.2
Zhang, C.3
Sugimori, M.4
-
332
-
-
0036708447
-
Bridging implicit and explicit solvent approaches for membrane electrostatics
-
Lin J-H, Baker N A and McCammon J A 2002 Bridging implicit and explicit solvent approaches for membrane electrostatics Biophys. J. 83 1374-9 (Pubitemid 34977711)
-
(2002)
Biophysical Journal
, vol.83
, Issue.3
, pp. 1374-1379
-
-
Lin, J.-H.1
Baker, N.A.2
Andrew McCammon, J.3
-
333
-
-
0031234042
-
An integral equation to describe the solvation of polar molecules in liquid water
-
Beglov D and Roux B 1997 An integral equation to describe the solvation of polar molecules in liquid water J. Phys. Chem. B 101 7821-6 (Pubitemid 127591348)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.39
, pp. 7821-7826
-
-
Beglov, D.1
Roux, B.2
-
334
-
-
0033007964
-
Integral equation theories for predicting water structure around molecules
-
DOI 10.1016/S0301-4622(99)00008-3, PII S0301462299000083
-
Liu Y and Ichiye T 1999 Integral equation theories for predicting water structure around molecules Biophys. Chem. 78 97-111 (Pubitemid 29206660)
-
(1999)
Biophysical Chemistry
, vol.78
, Issue.1-2
, pp. 97-111
-
-
Liu, Y.1
Ichiye, T.2
-
335
-
-
0031375133
-
Electrostatic potential and free energy of proteins: A comparison of the Poisson-Boltzmann and the Bogolyubov-Born-Green-Yvon equations
-
Gavryushov S and Zielenkiewicz P 1997 Electrostatic potential and free energy of proteins: a comparison of the Poisson-Boltzmann and the Bogolyubov-Born-Green-Yvon equations J. Phys. Chem. B 101 10903-9 (Pubitemid 127585245)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.50
, pp. 10903-10909
-
-
Gavryushov, S.1
Zielenkiewicz, P.2
-
336
-
-
0041375848
-
Ionic effects beyond Poisson-Boltzmann theory
-
Vlachy V 1999 Ionic effects beyond Poisson-Boltzmann theory Annu. Rev. Phys. Chem. 50 145-65 (Pubitemid 129565546)
-
(1999)
Annual Review of Physical Chemistry
, vol.50
, pp. 145-165
-
-
Vlachy, V.1
-
337
-
-
38949141177
-
Review: Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications
-
DOI 10.1002/bip.20877
-
Grochowski P and Trylska J 2007 Continuum molecular electrostatics, salt effects and counterion binding - a review of the Poisson-Boltzmann theory and its modifications Biopolymers 89 93-113 (Pubitemid 351211641)
-
(2008)
Biopolymers
, vol.89
, Issue.2
, pp. 93-113
-
-
Grochowski, P.1
Trylska, J.2
-
338
-
-
6244273869
-
Steric effects in electrolytes: A modified Poisson-Boltzmann equation
-
Borukhov I, Andelman D and Orland H 1997 Steric effects in electrolytes: a modified Poisson-Boltzmann equation Phys. Rev. Lett. 79 435-8 (Pubitemid 127653641)
-
(1997)
Physical Review Letters
, vol.79
, Issue.3
, pp. 435-438
-
-
Borukhov, I.1
Andelman, D.2
Orland, H.3
-
339
-
-
0020500271
-
Recent progress in the theory of the electric double layer
-
DOI 10.1016/0079-6816(83)90004-7
-
Henderson D 1983 Recent progress in the theory of the electric double layer Prog. Surf. Sci. 13 197-224 (Pubitemid 13557101)
-
(1983)
Progress in Surface Science
, vol.13
, Issue.3
, pp. 197-224
-
-
Henderson, D.1
-
340
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
10.1016/0022-2836(76)90311-9 0022-2836
-
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. 103 227-49
-
(1976)
J. Mol. Biol.
, vol.103
, Issue.2
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
341
-
-
0000115003
-
A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
-
10.1063/1.462997 0021-9606
-
Lee F S and Warshel A 1992 A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations J. Chem. Phys. 97 3100-7
-
(1992)
J. Chem. Phys.
, vol.97
, Issue.5
, pp. 3100-3107
-
-
Lee, F.S.1
Warshel, A.2
-
342
-
-
0000728542
-
Microscopic and semi-microscopic calculations of electrostatic energies in proteins by the polaris and enzymix programs
-
10.1002/jcc.540140205 0192-8651
-
Lee F S, Chu Z T and Warshel A 1993 Microscopic and semi-microscopic calculations of electrostatic energies in proteins by the polaris and enzymix programs J. Comput. Chem. 14 161-85
-
(1993)
J. Comput. Chem.
, vol.14
, Issue.2
, pp. 161-185
-
-
Lee, F.S.1
Chu, Z.T.2
Warshel, A.3
-
343
-
-
0030828226
-
The reorganization energy of cytochrome c revisited
-
Muegge I, Qi P X, Wand A J, Chu Z T and Warshel A 1997 The reorganization energy of cytochrome c revisited J. Phys. Chem. B 101 825-36 (Pubitemid 127627952)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.5
, pp. 825-836
-
-
Muegge, I.1
Qi, P.X.2
Wand, A.J.3
Chu, Z.T.4
Warshel, A.5
-
344
-
-
0000671518
-
a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches
-
Sham Y Y, Chu Z T and Warshel A 1997 Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches J. Phys. Chem. B 101 4458-72 (Pubitemid 127627868)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.22
, pp. 4458-4472
-
-
Sham, Y.Y.1
Chu, Z.T.2
Warshel, A.3
-
345
-
-
0010624785
-
The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins
-
Sham Y Y, Muegge I and Warshel A 1998 The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins Biophys. J. 74 1744-53 (Pubitemid 28157913)
-
(1998)
Biophysical Journal
, vol.74
, Issue.4
, pp. 1744-1753
-
-
Sham, Y.Y.1
Muegge, I.2
Warshel, A.3
-
346
-
-
0024293878
-
Why ion pair reversal by protein engineering is unlikely to succeed
-
10.1038/334270a0 0028-0836
-
Hwang J-K and Warshel A 1988 Why ion pair reversal by protein engineering is unlikely to succeed Nature 334 270-2
-
(1988)
Nature
, vol.334
, Issue.6179
, pp. 270-272
-
-
Hwang, J.-K.1
Warshel, A.2
-
348
-
-
34247596467
-
Electrostatic contributions to protein stability and folding energy
-
DOI 10.1016/j.febslet.2007.04.025, PII S0014579307004103
-
Roca M, Messer B and Warshel A 2007 Electrostatic contributions to protein stability and folding energy FEBS Lett. 581 2065-71 (Pubitemid 46671634)
-
(2007)
FEBS Letters
, vol.581
, Issue.10
, pp. 2065-2071
-
-
Roca, M.1
Messer, B.2
Warshel, A.3
-
349
-
-
0025891413
-
Electrostatic energy and macromolecular function
-
10.1146/annurev.bb.20.060191.001411 0883-9182
-
Warshel A and Åqvist J 1991 Electrostatic energy and macromolecular function Annu. Rev. Biophys. Biophys. Chem. 20 267-98
-
(1991)
Annu. Rev. Biophys. Biophys. Chem.
, vol.20
, Issue.1
, pp. 267-298
-
-
Warshel, A.1
Åqvist, J.2
-
350
-
-
0032054517
-
Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
-
DOI 10.1016/S0959-440X(98)80041-9
-
Warshel A and Papazyan A 1998 Electrostatic effects in macromolecules: fundamental concepts and practical modeling Curr. Opin. Struct. Biol. 8 211-7 (Pubitemid 28221053)
-
(1998)
Current Opinion in Structural Biology
, vol.8
, Issue.2
, pp. 211-217
-
-
Warshel, A.1
Papazyan, A.2
-
351
-
-
0037084491
-
Nonlinear response effects in continuum models of the hydration of ions
-
DOI 10.1063/1.1435566
-
Sandberg L and Edholm O 2002 Nonlinear response effects in continuum models of the hydration of ions J. Chem. Phys. 116 2936-44 (Pubitemid 34198148)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.7
, pp. 2936-2944
-
-
Sandberg, L.1
Edholm, O.2
-
352
-
-
84961980883
-
Calculated hydration free energies of small organic molecules using a nonlinear dielectric continuum model
-
DOI 10.1021/jp020434b
-
Sandberg L, Casemyr R and Edholm O 2002 Calculated hydration free energies of small organic molecules using a nonlinear dielectric continuum model J. Phys. Chem. B 106 7889-97 (Pubitemid 35382981)
-
(2002)
Journal of Physical Chemistry B
, vol.106
, Issue.32
, pp. 7889-7897
-
-
Sandberg, L.1
Casemyr, R.2
Edholm, O.3
-
353
-
-
38349111398
-
Solvation effect on conformations of 1,2:dimethoxyethane: Charge-dependent nonlinear response in implicit solvent models
-
10.1063/1.2815764 0021-9606 034501
-
Jha A K and Freed K F 2008 Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models J. Chem. Phys. 128 034501
-
(2008)
J. Chem. Phys.
, vol.128
, Issue.3
-
-
Jha, A.K.1
Freed, K.F.2
-
354
-
-
49649108879
-
Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
-
10.1073/pnas.0804506105 0027-8424
-
Gong H, Hocky G and Freed K F 2008 Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model Proc. Natl Acad. Sci. USA 105 11146-51
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, Issue.32
, pp. 11146-11151
-
-
Gong, H.1
Hocky, G.2
Freed, K.F.3
-
355
-
-
61349086145
-
Langevin-Debye model for nonlinear electrostatic screening of solvated ions
-
10.1103/PhysRevLett.102.057603 0031-9007 057603
-
Gong H and Freed K F 2009 Langevin-Debye model for nonlinear electrostatic screening of solvated ions Phys. Rev. Lett. 102 057603
-
(2009)
Phys. Rev. Lett.
, vol.102
, Issue.5
-
-
Gong, H.1
Freed, K.F.2
-
356
-
-
76249089135
-
Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: Salt bridges can stabilize proteins
-
10.1016/j.bpj.2009.10.031 0006-3495
-
Gong H and Freed K F 2010 Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins Biophys. J. 98 470-7
-
(2010)
Biophys. J.
, vol.98
, Issue.3
, pp. 470-477
-
-
Gong, H.1
Freed, K.F.2
-
357
-
-
0039553312
-
Polar solvent structure in the theory of ionic solvation
-
10.1039/f29747001121 0300-9238 II
-
Dogonadze R R and Kornyshev A A 1974 Polar solvent structure in the theory of ionic solvation J. Chem. Soc. Faraday Trans. II 70 1121-32
-
(1974)
J. Chem. Soc. Faraday Trans.
, vol.70
, pp. 1121-1132
-
-
Dogonadze, R.R.1
Kornyshev, A.A.2
-
359
-
-
69449087340
-
Nonlocal optical response of metal nanostructures with arbitrary shape
-
10.1103/PhysRevLett.103.097403 0031-9007 097403
-
McMahon J M, Gray S K and Schatz G C 2009 Nonlocal optical response of metal nanostructures with arbitrary shape Phys. Rev. Lett. 103 097403
-
(2009)
Phys. Rev. Lett.
, vol.103
, Issue.9
-
-
McMahon, J.M.1
Gray, S.K.2
Schatz, G.C.3
-
360
-
-
33845545452
-
Analysis of nonlocal electrostatic effects in chiral smectic C liquid crystals
-
DOI 10.1137/050641120
-
Park J and Calderer M C 2006 Analysis of nonlocal electrostatic effects in chiral smectic c liquid crystals SIAM J. Appl. Math. 66 2107 (Pubitemid 44925764)
-
(2006)
SIAM Journal on Applied Mathematics
, vol.66
, Issue.6
, pp. 2107-2126
-
-
Park, J.1
Calderer, M.C.2
-
361
-
-
33847735473
-
Calibration of nonlocal scaling effect parameter for free vibration of carbon nanotubes by molecular dynamics
-
DOI 10.1063/1.2423140
-
Duan W H, Wang C M and Zhang Y Y 2007 Calibration of nonlocal scaling effect parameter for free vibration of carbon nanotubes by molecular dynamics J. Appl. Phys. 101 024305 (Pubitemid 46372839)
-
(2007)
Journal of Applied Physics
, vol.101
, Issue.2
, pp. 024305
-
-
Duan, W.H.1
Wang, C.M.2
Zhang, Y.Y.3
-
362
-
-
84962362083
-
An advanced continuum medium model for treating solvation effects:
-
10.1063/1.472193 0021-9606
-
Basilevsky M V and Parsons D F 1996 An advanced continuum medium model for treating solvation effects: nonlocal electrostatics with a cavity J. Chem. Phys. 105 3734
-
(1996)
J. Chem. Phys.
, vol.105
, Issue.9
, pp. 3734
-
-
Basilevsky, M.V.1
Parsons, D.F.2
-
363
-
-
7544234545
-
Continuum equations for dielectric response to macro-molecular assemblies at the nano scale
-
DOI 10.1088/0305-4470/37/41/012, PII S0305447004806000
-
Scott R, Boland M, Rogale K and Fernandez A 2004 Continuum equations for dielectric response to macro-molecular assemblies at the nano scale J. Phys. A: Math. Gen. 37 9791 (Pubitemid 39453555)
-
(2004)
Journal of Physics A: Mathematical and General
, vol.37
, Issue.41
, pp. 9791-9803
-
-
Scott, R.1
Boland, M.2
Rogale, K.3
Fernandez, A.4
-
364
-
-
4444238115
-
Influence of the solvent structure on the interactions in proteins
-
DOI 10.1529/biophysj.103.038620
-
Rubinstein A and Sherman S 2004 Influence of the solvent structure on the electrostatic interactions in proteins Biophys. J. 87 1544-57 (Pubitemid 39167013)
-
(2004)
Biophysical Journal
, vol.87
, Issue.3
, pp. 1544-1557
-
-
Rubinstein, A.1
Sherman, S.2
-
365
-
-
34948897088
-
Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach
-
DOI 10.1002/bip.20808
-
Rubinstein A and Sherman S 2007 Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach Biopolymers 87 149-64 (Pubitemid 47518366)
-
(2007)
Biopolymers
, vol.87
, Issue.2-3
, pp. 149-164
-
-
Rubinstein, A.1
Sherman, S.2
-
366
-
-
77956102305
-
Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach
-
10.1103/PhysRevE.82.021915 1539-3755 E 021915
-
Rubinstein A, Sabirianov R, Mei W, Namavar F and Khoynezhad A 2010 Effect of the ordered interfacial water layer in protein complex formation: a nonlocal electrostatic approach Phys. Rev. E 82 021915
-
(2010)
Phys. Rev.
, vol.82
, Issue.2
-
-
Rubinstein, A.1
Sabirianov, R.2
Mei, W.3
Namavar, F.4
Khoynezhad, A.5
-
367
-
-
0002002590
-
Critical comments on the nonlocal dielectric function employed in recent theories of the hydration force
-
10.1016/0009-2614(90)87218-G 0009-2614
-
Attard P, Wei D and Patey G N 1990 Critical comments on the nonlocal dielectric function employed in recent theories of the hydration force Chem. Phys. Lett. 172 69-72
-
(1990)
Chem. Phys. Lett.
, vol.172
, Issue.1
, pp. 69-72
-
-
Attard, P.1
Wei, D.2
Patey, G.N.3
-
368
-
-
19544375042
-
Novel formulation of nonlocal electrostatics
-
10.1103/PhysRevLett.93.108104 0031-9007 108104
-
Hildebrandt A, Blossey R, Rjasanow S, Kohlbacher O and Lenhof H-P 2004 Novel formulation of nonlocal electrostatics Phys. Rev. Lett. 93 108104
-
(2004)
Phys. Rev. Lett.
, vol.93
, Issue.10
-
-
Hildebrandt, A.1
Blossey, R.2
Rjasanow, S.3
Kohlbacher, O.4
Lenhof, H.-P.5
-
369
-
-
78651385210
-
Slits, plates and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics
-
10.1103/PhysRevE.82.052501 1539-3755 E 052501
-
Paillusson F and Blossey R 2010 Slits, plates and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics Phys. Rev. E 82 052501
-
(2010)
Phys. Rev.
, vol.82
, Issue.5
-
-
Paillusson, F.1
Blossey, R.2
-
370
-
-
33846683115
-
Electrostatic potentials of proteins in water: A structured continuum approach
-
DOI 10.1093/bioinformatics/btl312
-
Hildebrandt A, Blossey R, Rjasanow S, Kohlbacher O and Lenhof H-P 2007 Electrostatic potentials of proteins in water: a structured continuum approach Bioinformatics 23 e99-103 (Pubitemid 46189642)
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Hildebrandt, A.1
Blossey, R.2
Rjasanow, S.3
Kohlbacher, O.4
Lenhof, H.-P.5
-
371
-
-
77950048769
-
A new numerical method for nonlocal electrostatics in biomolecular simulations
-
10.1016/j.jcp.2010.01.040 0021-9991
-
Weggler S, Rutka V and Hildebrandt A 2010 A new numerical method for nonlocal electrostatics in biomolecular simulations J. Comput. Phys. 229 4059-74
-
(2010)
J. Comput. Phys.
, vol.229
, Issue.11
, pp. 4059-4074
-
-
Weggler, S.1
Rutka, V.2
Hildebrandt, A.3
-
373
-
-
80052950348
-
Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins
-
10.1063/1.3632995 0021-9606 104113
-
Bardhan J P 2011 Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins J. Chem. Phys. 135 104113
-
(2011)
J. Chem. Phys.
, vol.135
, Issue.10
-
-
Bardhan, J.P.1
-
374
-
-
76749157270
-
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation
-
10.1063/1.3298862 0021-9606 064101
-
Koehl P and Delarue M 2010 AQUASOL: an efficient solver for the dipolar Poisson-Boltzmann-Langevin equation J. Chem. Phys. 132 064101
-
(2010)
J. Chem. Phys.
, vol.132
, Issue.6
-
-
Koehl, P.1
Delarue, M.2
-
375
-
-
33644682762
-
Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models
-
DOI 10.1103/PhysRevLett.96.087802, 087802
-
Dzubiella J, Swanson J M J and McCammon J A 2006 Coupling hydrophobicity, dispersion and electrostatics in continuum solvent models Phys. Rev. Lett. 96 087802 (Pubitemid 43334270)
-
(2006)
Physical Review Letters
, vol.96
, Issue.8
, pp. 1-4
-
-
Dzubiella, J.1
Swanson, J.M.J.2
McCammon, J.A.3
-
376
-
-
41349089274
-
Density functional theory of solvation in a polar solvent: Extracting the functional from homogeneous solvent simulations
-
DOI 10.1103/PhysRevE.66.031206, 031206
-
Ramirez R, Gebauer R, Mareschal M and Borgis D 2002 Density functional theory of solvation in a polar solvent: extracting the functional from homogeneous solvent simulations Phys. Rev. E 66 031206 (Pubitemid 40606372)
-
(2002)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.66
, Issue.3
-
-
Ramirez, R.1
Gebauer, R.2
Mareschal, M.3
Borgis, D.4
-
377
-
-
17444404197
-
Density functional theory of solvation and its relation to implicit solvent models
-
DOI 10.1021/jp045453v
-
Ramirez R and Borgis D 2005 Density functional theory of solvation and its relation to implicit solvent models J. Phys. Chem. B 109 6754-63 (Pubitemid 40538444)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.14
, pp. 6754-6763
-
-
Ramirez, R.1
Borgis, D.2
-
378
-
-
0037078433
-
Structure and effective interactions in multi-component hard-sphere liquids: The fundamental-measure density functional approach
-
DOI 10.1088/0953-8984/14/40/308, PII S0953898402350264, Liquid State Theory, from White Dwarfs to Colloids
-
Rosenfeld Y 2002 Structure and effective interactions in multi-component hard-sphere liquids: the fundamental-measure density functional approach J. Phys.: Condens. Matter 14 9141-52 (Pubitemid 35275044)
-
(2002)
Journal of Physics Condensed Matter
, vol.14
, Issue.40
, pp. 9141-9152
-
-
Rosenfeld, Y.1
-
379
-
-
24444431754
-
Density functional theory of molecular fluids: Free-energy model for the inhomogeneous hard-body fluid
-
10.1103/PhysRevE.50.R3318 1063-651X E
-
Rosenfeld Y 1994 Density functional theory of molecular fluids: free-energy model for the inhomogeneous hard-body fluid Phys. Rev. E 50 R3318-21
-
(1994)
Phys. Rev.
, vol.50
, Issue.5
-
-
Rosenfeld, Y.1
-
380
-
-
0030286908
-
Geometrically based density functional theory of liquids
-
Rosenfeld Y 1996 Geometrically based density functional theory of liquids J. Phys.: Condens. Matter 8 9289-92 (Pubitemid 126588474)
-
(1996)
Journal of Physics Condensed Matter
, vol.8
, Issue.47
, pp. 9289-9292
-
-
Rosenfeld, Y.1
-
381
-
-
0035420557
-
Weighted density functional theory of the solvophobic effect
-
10.1103/PhysRevE.64.021512 1063-651X E 021512
-
Sun S X 2001 Weighted density functional theory of the solvophobic effect Phys. Rev. E 64 021512
-
(2001)
Phys. Rev.
, vol.64
, Issue.2
-
-
Sun, S.X.1
-
382
-
-
0032568751
-
Three-dimensional density profiles of water in contact with a solute of arbitrary shape: A RISM approach
-
PII S0009261498004710
-
Kovalenko A and Hirata F 1998 Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach Chem. Phys. Lett. 290 237-44 (Pubitemid 128186056)
-
(1998)
Chemical Physics Letters
, vol.290
, Issue.1-3
, pp. 237-244
-
-
Kovalenko, A.1
Hirata, F.2
-
383
-
-
0033691158
-
Potentials of mean force of simple ions in ambient aqueous solution: I. Three-dimensional reference interaction site model approach
-
10.1063/1.481676 0021-9606
-
Kovalenko A and Hirata F 2000 Potentials of mean force of simple ions in ambient aqueous solution: I. Three-dimensional reference interaction site model approach J. Chem. Phys. 112 10391-402
-
(2000)
J. Chem. Phys.
, vol.112
, Issue.23
, pp. 10391-10402
-
-
Kovalenko, A.1
Hirata, F.2
-
384
-
-
41549158650
-
Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution
-
DOI 10.1002/jcc.20844
-
Miyata T and Hirata F 2008 Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution J. Comput. Chem. 29 871-82 (Pubitemid 351473683)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.6
, pp. 871-882
-
-
Miyata, T.1
Hirata, F.2
-
385
-
-
51749093938
-
A molecular site-site integral equation that yields the dielectric constant
-
10.1063/1.2976580 0021-9606 104512
-
Dyer K M, Perkyns J S, Stell G and Pettitt B M 2008 A molecular site-site integral equation that yields the dielectric constant J. Chem. Phys. 129 104512
-
(2008)
J. Chem. Phys.
, vol.129
, Issue.10
-
-
Dyer, K.M.1
Perkyns, J.S.2
Stell, G.3
Pettitt, B.M.4
-
386
-
-
61949186554
-
Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids
-
10.1021/jp807068k 1520-6106 B
-
Yoshida N, Imai T, Phongphanphanee S, Kovalenko A and Hirata F 2009 Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids J. Phys. Chem. B 113 873-86
-
(2009)
J. Phys. Chem.
, vol.113
, Issue.4
, pp. 873-886
-
-
Yoshida, N.1
Imai, T.2
Phongphanphanee, S.3
Kovalenko, A.4
Hirata, F.5
-
387
-
-
3242675766
-
A fast solver for the Ornstein-Zernike equations
-
DOI 10.1016/j.jcp.2003.12.006, PII S002199910300648X
-
Kelley C T and Pettitt B M 2004 A fast solver for the Ornstein-Zernike equations J. Comput. Phys. 197 491-501 (Pubitemid 38955944)
-
(2004)
Journal of Computational Physics
, vol.197
, Issue.2
, pp. 491-501
-
-
Kelley, C.T.1
Pettitt, B.M.2
-
388
-
-
60349130039
-
A highly parallelizable integral equation theory for three dimensional solvent distribution function: Application to biomolecules
-
10.1063/1.3077209 0021-9606 064111
-
Yokogawa D, Sato H, Imai T and Sakaki S 2009 A highly parallelizable integral equation theory for three dimensional solvent distribution function: application to biomolecules J. Chem. Phys. 130 064111
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.6
-
-
Yokogawa, D.1
Sato, H.2
Imai, T.3
Sakaki, S.4
-
389
-
-
0004694653
-
Development of theories of inhomogeneous fluids
-
Rowlinson J S 1992 Development of theories of inhomogeneous fluids Fundamentals of Inhomogeneous Fluids ed D Henderson (New York: Dekker) pp 1-22
-
(1992)
Fundamentals of Inhomogeneous Fluids
, pp. 1-22
-
-
Rowlinson, J.S.1
-
390
-
-
0001409388
-
On the theory of strong electrolyte solutions
-
10.1063/1.1749393 0021-9606
-
Kirkwood J G 1934 On the theory of strong electrolyte solutions J. Chem. Phys. 2 767-72
-
(1934)
J. Chem. Phys.
, vol.2
, Issue.11
, pp. 767-772
-
-
Kirkwood, J.G.1
-
391
-
-
0011136976
-
Extension of the Debye-Hückel theory of electrolyte solutions
-
10.1063/1.1671378 0021-9606
-
Outhwaite C W 1969 Extension of the Debye-Hückel theory of electrolyte solutions J. Chem. Phys. 50 2277-89
-
(1969)
J. Chem. Phys.
, vol.50
, Issue.6
, pp. 2277-2289
-
-
Outhwaite, C.W.1
-
392
-
-
33646383086
-
Comparison of density functional and modified Poisson-Boltzmann structural properties for a spherical double layer
-
Bhuiyan L B and Outhwaite C W 2005 Comparison of density functional and modified Poisson-Boltzmann structural properties for a spherical double layer Condens. Matter Phys. 8 287-302 (available at http://www.icmp.lviv.ua/journal/ zbirnyk.42/) (Pubitemid 43664307)
-
(2005)
Condensed Matter Physics
, vol.8
, Issue.2
, pp. 287-302
-
-
Bhuiyan, L.B.1
Outhwaite, C.W.2
-
393
-
-
58249143655
-
Comparison of exclusion volume corrections to the Poisson-Boltzmann equation for inhomogeneous electrolytes
-
10.1016/j.jcis.2008.11.059 0021-9797
-
Bhuiyan L B and Outhwaite C W 2009 Comparison of exclusion volume corrections to the Poisson-Boltzmann equation for inhomogeneous electrolytes J. Colloid Interface Sci. 331 543-7
-
(2009)
J. Colloid Interface Sci.
, vol.331
, Issue.2
, pp. 543-547
-
-
Bhuiyan, L.B.1
Outhwaite, C.W.2
-
394
-
-
0001837839
-
Multi-multigrid solution of modified Poisson-Boltzmann equation for arbitrarily shaped molecules
-
10.1002/(SICI)1096-987X(199806)19:8<893::AID-JCC8>3.0.CO;2-K 0192-8651
-
Tomac S and Gräslund A 1998 Multi-multigrid solution of modified Poisson-Boltzmann equation for arbitrarily shaped molecules J. Comput. Chem. 19 893-901
-
(1998)
J. Comput. Chem.
, vol.19
, Issue.8
, pp. 893-901
-
-
Tomac, S.1
Gräslund, A.2
-
395
-
-
79959636026
-
Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes: II. Size effects on ionic distributions and diffusion-reaction rates
-
10.1016/j.bpj.2011.03.059 0006-3495
-
Lu B and Zhou Y C 2011 Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes: II. Size effects on ionic distributions and diffusion-reaction rates Biophys. J. 100 2475-85
-
(2011)
Biophys. J.
, vol.100
, Issue.10
, pp. 2475-2485
-
-
Lu, B.1
Zhou, Y.C.2
-
396
-
-
36048952831
-
Evaluation of ion binding to DNA duplexes using a size-modified poisson-Boltzmann theory
-
DOI 10.1529/biophysj.106.099168
-
Chu V B, Bai Y, Lipfert J, Herschlag D and Doniach S 2007 Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory Biophys. J. 93 3202-9 (Pubitemid 350097110)
-
(2007)
Biophysical Journal
, vol.93
, Issue.9
, pp. 3202-3209
-
-
Chu, V.B.1
Bai, Y.2
Lipfert, J.3
Herschlag, D.4
Doniach, S.5
-
397
-
-
67650721206
-
Continuum electrostatics for ionic solutions with non-uniform ionic sizes
-
10.1088/0951-7715/22/4/007 0951-7715
-
Li B 2009 Continuum electrostatics for ionic solutions with non-uniform ionic sizes Nonlinearity 22 811-33
-
(2009)
Nonlinearity
, vol.22
, Issue.4
, pp. 811-833
-
-
Li, B.1
-
398
-
-
80051618654
-
Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach
-
10.1103/PhysRevE.84.021901 1539-3755 E 021901
-
Zhou S, Wang Z and Li B 2011 Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach Phys. Rev. E 84 021901
-
(2011)
Phys. Rev.
, vol.84
, Issue.2
-
-
Zhou, S.1
Wang, Z.2
Li, B.3
-
399
-
-
68949119467
-
Simple and robust solver for the Poisson-Boltzmann equation
-
10.1103/PhysRevE.80.016705 1539-3755 E 016705
-
Baptista M, Schmitz R and Dünweg B 2009 Simple and robust solver for the Poisson-Boltzmann equation Phys. Rev. E 80 016705
-
(2009)
Phys. Rev.
, vol.80
, Issue.1
-
-
Baptista, M.1
Schmitz, R.2
Dünweg, B.3
-
400
-
-
27944484382
-
Incorporation of excluded-volume correlations into Poisson-Boltzmann theory
-
DOI 10.1103/PhysRevE.71.061106, 061106
-
Antypov D, Barbosa M C and Holm C 2005 Incorporation of excluded-volume correlations into Poisson-Boltzmann theory Phys. Rev. E 71 061106 (Pubitemid 41663728)
-
(2005)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.71
, Issue.6
, pp. 1-10
-
-
Antypov, D.1
Barbosa, M.C.2
Holm, C.3
-
401
-
-
79955811772
-
Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory
-
10.1016/j.jcis.2011.03.088 0021-9797
-
Gillespie D, Khair A S, Bardhan J P and Pennathur S 2011 Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory J. Colloid Interface Sci. 359 520-9
-
(2011)
J. Colloid Interface Sci.
, vol.359
, Issue.2
, pp. 520-529
-
-
Gillespie, D.1
Khair, A.S.2
Bardhan, J.P.3
Pennathur, S.4
-
402
-
-
0037175732
-
Coupling poisson-nernst-planck and density functional theory to calculate ion flux
-
DOI 10.1088/0953-8984/14/46/317, PII S0953898402378986
-
Gillespie D, Nonner W and Eisenberg R S 2002 Coupling Poisson-Nernst-Planck and density functional theory to calculate ion flux J. Phys.: Condens. Matter 14 12129-45 (Pubitemid 35434013)
-
(2002)
Journal of Physics Condensed Matter
, vol.14
, Issue.46
, pp. 12129-12145
-
-
Gillespie, D.1
Nonner, W.2
Eisenberg, R.S.3
-
403
-
-
38949090423
-
Energetics of divalent selectivity in a calcium channel: The ryanodine receptor case study
-
10.1529/biophysj.107.116798 0006-3495
-
Gillespie D 2008 Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study Biophys. J. 94 1169-84
-
(2008)
Biophys. J.
, vol.94
, Issue.4
, pp. 1169-1184
-
-
Gillespie, D.1
-
404
-
-
33244495289
-
Physics of size selectivity
-
DOI 10.1103/PhysRevLett.95.247801
-
Roth R and Gillespie D 2005 Physics of size selectivity Phys. Rev. Lett. 95 247801 (Pubitemid 43272913)
-
(2005)
Physical Review Letters
, vol.95
, Issue.24
, pp. 247801
-
-
Roth, R.1
Gillespie, D.2
-
406
-
-
33751104241
-
Computational investigations of pore forming peptide assemblies in lipid bilayers
-
DOI 10.1103/PhysRevLett.97.208701
-
Frink L J D and Frischknecht A L 2006 Computational investigations of pore forming peptide assemblies in lipid bilayers Phys. Rev. Lett. 97 208701 (Pubitemid 44771653)
-
(2006)
Physical Review Letters
, vol.97
, Issue.20
, pp. 208701
-
-
Frink, L.J.D.1
Frischknecht, A.L.2
-
407
-
-
4244202584
-
Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing
-
10.1103/PhysRevLett.63.980 0031-9007
-
Rosenfeld Y 1989 Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing Phys. Rev. Lett. 63 980-3
-
(1989)
Phys. Rev. Lett.
, vol.63
, Issue.9
, pp. 980-983
-
-
Rosenfeld, Y.1
-
408
-
-
0242493974
-
Density functional theory of charged, hard-sphere fluids
-
10.1103/PhysRevE.68.031503 1063-651X E 031503
-
Gillespie D, Nonner W and Eisenberg R S 2003 Density functional theory of charged, hard-sphere fluids Phys. Rev. E 68 031503
-
(2003)
Phys. Rev.
, vol.68
, Issue.3
-
-
Gillespie, D.1
Nonner, W.2
Eisenberg, R.S.3
-
409
-
-
42749106873
-
Density-functional theory for the structures and thermodynamic properties of highly asymmetric electrolyte and neutral component mixtures
-
10.1103/PhysRevE.70.031109 1539-3755 E 031109
-
Li Z and Wu J 2004 Density-functional theory for the structures and thermodynamic properties of highly asymmetric electrolyte and neutral component mixtures Phys. Rev. E 70 031109
-
(2004)
Phys. Rev.
, vol.70
, Issue.3
-
-
Li, Z.1
Wu, J.2
-
410
-
-
0041856288
-
A new efficient method for density functional theory calculations of inhomogeneous fluids
-
DOI 10.1016/S0021-9991(03)00270-5
-
Sears M P and Frink L J D 2003 A new efficient method for density functional theory calculations of inhomogeneous fluids J. Comput. Phys. 190 184-200 (Pubitemid 37064982)
-
(2003)
Journal of Computational Physics
, vol.190
, Issue.1
, pp. 184-200
-
-
Sears, M.P.1
Frink, L.J.D.2
-
411
-
-
42449112426
-
Parallel segregated Schur complement methods for fluid density functional theories
-
10.1137/060661594 1064-8275
-
Heroux M A, Salinger A G and Frink L J D 2007 Parallel segregated Schur complement methods for fluid density functional theories SIAM J. Sci. Comput. 29 2059-77
-
(2007)
SIAM J. Sci. Comput.
, vol.29
, Issue.5
, pp. 2059-2077
-
-
Heroux, M.A.1
Salinger, A.G.2
Frink, L.J.D.3
-
412
-
-
77950393263
-
An efficient algorithm for classical density functional theory in three dimensions: Ionic solutions
-
10.1063/1.3357981 0021-9606 124101
-
Knepley M G, Karpeev D A, Davidovits S, Eisenberg R S and Gillespie D 2010 An efficient algorithm for classical density functional theory in three dimensions: ionic solutions J. Chem. Phys. 132 124101
-
(2010)
J. Chem. Phys.
, vol.132
, Issue.12
-
-
Knepley, M.G.1
Karpeev, D.A.2
Davidovits, S.3
Eisenberg, R.S.4
Gillespie, D.5
-
413
-
-
0037175696
-
Density functional theory of inhomogeneous classical fluids: Recent developments and new perspectives
-
Löwen H 1905 2002 Density functional theory of inhomogeneous classical fluids: recent developments and new perspectives J. Phys.: Condens. Matter 14 11897-905
-
(1905)
J. Phys.: Condens. Matter
, vol.14
, pp. 11897-11905
-
-
Löwen, H.1
-
414
-
-
0037175695
-
Numerical challenges in the application of density functional theory to biology and nanotechnology
-
DOI 10.1088/0953-8984/14/46/320, PII S0953898402377750
-
Frink L J D, Salinger A G, Sears M P, Weinhold J D and Frischknecht A L 2002 Numerical challenges in the application of density functional theory to biology and nanotechnology J. Phys.: Condens. Matter 14 12167-87 (Pubitemid 35434016)
-
(2002)
Journal of Physics Condensed Matter
, vol.14
, Issue.46
, pp. 12167-12187
-
-
Frink, L.J.D.1
Salinger, A.G.2
Sears, M.P.3
Weinhold, J.D.4
Frischknecht, A.L.5
-
415
-
-
33846978150
-
Density-functional theory for complex fluids
-
DOI 10.1146/annurev.physchem.58.032806.104650
-
Wu J and Li Z 2007 Density-functional theory for complex fluids Annu. Rev. Phys. Chem. 58 85-112 (Pubitemid 46877586)
-
(2007)
Annual Review of Physical Chemistry
, vol.58
, pp. 85-112
-
-
Wu, J.1
Li, Z.2
-
416
-
-
75649134244
-
Fundamental measure theory for hard-sphere mixtures: A review
-
0953-8984 063102
-
Roth R 2010 Fundamental measure theory for hard-sphere mixtures: a review J. Phys.: Condens. Matter 22 063102
-
(2010)
J. Phys.: Condens. Matter
, vol.22
, Issue.6
-
-
Roth, R.1
-
417
-
-
36749119973
-
Deformable stochastic boundaries in molecular dynamics
-
10.1063/1.445724 0021-9606
-
Brooks C L III and Karplus M 1983 Deformable stochastic boundaries in molecular dynamics J. Chem. Phys. 79 6312-25
-
(1983)
J. Chem. Phys.
, vol.79
, Issue.12
, pp. 6312-6325
-
-
Brooks, C.L.1
Karplus, M.2
-
418
-
-
0001655657
-
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
-
10.1063/1.466711 0021-9606
-
Beglov D and Roux B 1994 Finite representation of an infinite bulk system: solvent boundary potential for computer simulations J. Chem. Phys. 100 9050-63
-
(1994)
J. Chem. Phys.
, vol.100
, Issue.12
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
419
-
-
0035249196
-
Generalized solvent boundary potential for computer simulations
-
DOI 10.1063/1.1336570
-
Im W, Bernèche S and Roux B 2001 Generalized solvent boundary potential for computer simulations J. Chem. Phys. 114 2924-37 (Pubitemid 32253408)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.7
, pp. 2924-2937
-
-
Im, W.1
Berneche, S.2
Roux, B.3
-
420
-
-
0037109541
-
Electrostatic free energy calculations using the generalized solvent boundary potential method
-
DOI 10.1063/1.1507108
-
Banavali N K, Im W and Roux B 2002 Electrostatic free energy calculations using the generalized solvent boundary potential method J. Chem. Phys. 117 7381-9 (Pubitemid 35354184)
-
(2002)
Journal of Chemical Physics
, vol.117
, Issue.15
, pp. 7381-7388
-
-
Banavali, N.K.1
Im, W.2
Roux, B.3
-
421
-
-
58149154650
-
Efficiency and accuracy of the generalized solvent boundary potential for hybrid QM/MM simulations: Implementation for semiempirical Hamiltonians
-
10.1021/ct800193a 1549-9618
-
Benighaus T and Thiel W 2008 Efficiency and accuracy of the generalized solvent boundary potential for hybrid QM/MM simulations: implementation for semiempirical Hamiltonians J. Chem. Theory Comput. 4 1600-9
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.10
, pp. 1600-1609
-
-
Benighaus, T.1
Thiel, W.2
-
422
-
-
79958816397
-
A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent
-
10.1063/1.3595262 0021-9606 214103
-
Wagoner J A and Pande V S 2011 A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent J. Chem. Phys. 134 214103
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.21
-
-
Wagoner, J.A.1
Pande, V.S.2
-
423
-
-
9244224092
-
An efficient hybrid explicit/implicit solvent method for biomolecular simulations
-
10.1002/jcc.20119 0192-8651
-
Lee M S, Salsbury F R Jr and Olson M A 2004 An efficient hybrid explicit/implicit solvent method for biomolecular simulations J. Comput. Chem. 25 1967-78
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.16
, pp. 1967-1978
-
-
Lee, M.S.1
Salsbury, F.R.2
Olson, M.A.3
-
424
-
-
84961981256
-
Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells
-
DOI 10.1063/1.2202356
-
Brancato G, Rega N and Barone V 2006 Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells J. Chem. Phys. 124 214505 (Pubitemid 43877822)
-
(2006)
Journal of Chemical Physics
, vol.124
, Issue.21
, pp. 214505
-
-
Brancato, G.1
Rega, N.2
Barone, V.3
-
425
-
-
33746349837
-
Elastic bag model for molecular dynamics simulations of solvated systems: Application to liquid water and solvated peptides
-
DOI 10.1021/jp057532s
-
Li Y, Krilov G and Berne B J 2006 Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides J. Phys. Chem. B 110 13256-63 (Pubitemid 44115664)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.26
, pp. 13256-13263
-
-
Li, Y.1
Krilov, G.2
Berne, B.J.3
-
426
-
-
33947198768
-
A boundary element formulation of protein electrostatics with explicit ions
-
10.1016/j.jcp.2006.09.011 0021-9991
-
Xin W and Juffer A H 2007 A boundary element formulation of protein electrostatics with explicit ions J. Comput. Phys. 223 416-35
-
(2007)
J. Comput. Phys.
, vol.223
, Issue.1
, pp. 416-435
-
-
Xin, W.1
Juffer, A.H.2
-
427
-
-
42149159601
-
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
-
DOI 10.1002/jcc.20874
-
Prabhu N V, Panda M, Yang Q and Sharp K A 2008 Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules J. Comput. Chem. 29 1113-30 (Pubitemid 351535409)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.7
, pp. 1113-1130
-
-
Prabhu, N.V.1
Panda, M.2
Yang, Q.3
Sharp, K.A.4
-
428
-
-
3042835846
-
Monte Carlo simulation study of a system With a dielectric boundary: Application to calcium channel selectivity
-
DOI 10.1080/0892702031000152226
-
Boda D, Varga T, Henderson D, Busath D, Nonner W, Gillespie D and Eisenberg B 2004 Monte Carlo simulation study of a system with a dielectric boundary: application to calcium channel selectivity Mol. Simul. 30 89-96 (Pubitemid 40026330)
-
(2004)
Molecular Simulation
, vol.30
, Issue.2-3
, pp. 89-96
-
-
Boda, D.1
Varga, T.2
Henderson, D.3
Busath, D.D.4
Nonner, W.5
Gillespie, D.6
Eisenberg, B.7
-
429
-
-
34548717678
-
Steric selectivity in Na channels arising from protein polarization and mobile side chains
-
DOI 10.1529/biophysj.107.105478
-
Boda D, Nonner W, Valiskó M, Henderson D, Eisenberg B and Gillespie D 2007 Steric selectivity in Na channels arising from protein polarization and mobile side chains Biophys. J. 93 1960-80 (Pubitemid 47437580)
-
(2007)
Biophysical Journal
, vol.93
, Issue.6
, pp. 1960-1980
-
-
Boda, D.1
Nonner, W.2
Valisko, M.3
Henderson, D.4
Eisenberg, B.5
Gillespie, D.6
Eisenberg, R.S.7
-
430
-
-
34247260951
-
Combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel
-
DOI 10.1103/PhysRevLett.98.168102
-
Boda D, Valiskó M, Eisenberg B, Nonner W, Henderson D and Gillespie D 2007 Combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel Phys. Rev. Lett. 92 168102 (Pubitemid 46609781)
-
(2007)
Physical Review Letters
, vol.98
, Issue.16
, pp. 168102
-
-
Boda, D.1
Valisko, M.2
Eisenberg, B.3
Nonner, W.4
Henderson, D.5
Gillespie, D.6
-
431
-
-
36849108886
-
Monte Carlo study of the thermodynamics of electrolyte solutions
-
10.1063/1.1672932 0021-9606
-
Card D N and Valleau J P 1970 Monte Carlo study of the thermodynamics of electrolyte solutions J. Chem. Phys. 52 6232-40
-
(1970)
J. Chem. Phys.
, vol.52
, Issue.12
, pp. 6232-6240
-
-
Card, D.N.1
Valleau, J.P.2
-
432
-
-
51149205918
-
What is 'liquid'? Understanding the states of matter
-
10.1103/RevModPhys.48.587 0034-6861
-
Barker J A and Henderson D 1976 What is 'liquid'? Understanding the states of matter Rev. Mod. Phys. 48 587-671
-
(1976)
Rev. Mod. Phys.
, vol.48
, Issue.4
, pp. 587-671
-
-
Barker, J.A.1
Henderson, D.2
-
433
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
DOI 10.1002/jcc.20291
-
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A E and Berendsen H J C 2005 GROMACS: fast, flexible and free J. Comput. Chem. 26 1701-18 (Pubitemid 43076182)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
434
-
-
79951777660
-
Treecode-based generalized born method
-
10.1063/1.3552945 0021-9606 064107
-
Xu Z, Cheng X and Yang H 2011 Treecode-based generalized born method J. Chem. Phys. 134 064107
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.6
-
-
Xu, Z.1
Cheng, X.2
Yang, H.3
-
435
-
-
64749108343
-
CUSA and CUDA: GPU-accelerated method for estimating solvent accessible surface area and desolvation
-
10.1089/cmb.2008.0157 1066-5277
-
Dynerman D, Butzlaff E and Mitchell J C 2009 CUSA and CUDA: GPU-accelerated method for estimating solvent accessible surface area and desolvation J. Comput. Biol. 16 523-37
-
(2009)
J. Comput. Biol.
, vol.16
, Issue.4
, pp. 523-537
-
-
Dynerman, D.1
Butzlaff, E.2
Mitchell, J.C.3
-
436
-
-
35948963714
-
Accelerating molecular modeling applications with graphics processors
-
DOI 10.1002/jcc.20829
-
Stone J E, Phillips J C, Freddolino P L, Hardy D J, Trabuco L G and Schulten K 2007 Accelerating molecular modeling applications with graphics processors J. Comput. Chem. 28 2618-40 (Pubitemid 350074136)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.16
, pp. 2618-2640
-
-
Stone, J.E.1
Phillips, J.C.2
Freddolino, P.L.3
Hardy, D.J.4
Trabuco, L.G.5
Schulten, K.6
-
438
-
-
64649105762
-
Accelerating molecular dynamics simulation on graphics processing units
-
10.1002/jcc.21209 0192-8651
-
Friedrichs M S, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg A L, Ensign D L, Bruns C M and Pande V S 2009 Accelerating molecular dynamics simulation on graphics processing units J. Comput. Chem. 30 864-72
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.6
, pp. 864-872
-
-
Friedrichs, M.S.1
Eastman, P.2
Vaidyanathan, V.3
Houston, M.4
Legrand, S.5
Beberg, A.L.6
Ensign, D.L.7
Bruns, C.M.8
Pande, V.S.9
-
439
-
-
80053970088
-
MOIL-opt: Energy-conserving molecular dynamics on a GPU/CPU system
-
10.1021/ct200360f 1549-9618
-
Ruymgaart A P, Cardenas A E and Elber R 2011 MOIL-opt: energy-conserving molecular dynamics on a GPU/CPU system J. Chem. Theory Comput. 7 3072-82
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.10
, pp. 3072-3082
-
-
Ruymgaart, A.P.1
Cardenas, A.E.2
Elber, R.3
-
440
-
-
77951978448
-
Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units
-
10.1016/j.jmgm.2010.04.001 1093-3263
-
Anandakrishnan R, Scogland T R W, Fenley A T, Gordon J C, Feng W and Onufriev A 2010 Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units J. Mol. Graph. Model. 28 904-10
-
(2010)
J. Mol. Graph. Model.
, vol.28
, Issue.8
, pp. 904-910
-
-
Anandakrishnan, R.1
Scogland, T.R.W.2
Fenley, A.T.3
Gordon, J.C.4
Feng, W.5
Onufriev, A.6
-
441
-
-
0035566962
-
Adaptive numerical treatment of elliptic systems on manifolds
-
DOI 10.1023/A:1014246117321
-
Holst M 2001 Adaptive numerical treatment of elliptic systems on manifolds Adv. Comput. Math. 15 139-91 (Pubitemid 33634300)
-
(2001)
Advances in Computational Mathematics
, vol.15
, Issue.1-4
, pp. 139-191
-
-
Holst, M.1
-
442
-
-
76249096812
-
DOLFIN: Automated finite element computing
-
10.1145/1731022.1731030 0098-3500
-
Logg A and Wells G N 2010 DOLFIN: automated finite element computing ACM Trans. Math. Softw. 37 20
-
(2010)
ACM Trans. Math. Softw.
, vol.37
, Issue.2
, pp. 1
-
-
Logg, A.1
Wells, G.N.2
-
445
-
-
34548709708
-
Efficient compilation of a class of variational forms
-
DOI 10.1145/1268769.1268771
-
Kirby R C and Logg A 2007 Efficient compilation of a class of variational forms ACM Trans. Math. Softw. 33 17 (Pubitemid 47424908)
-
(2007)
ACM Transactions on Mathematical Software
, vol.33
, Issue.3
, pp. 1268771
-
-
Kirby, R.C.1
Logg, A.2
-
446
-
-
48849098749
-
Benchmarking domain-specific compiler optimizations for variational forms
-
10.1145/1377612.1377614 0098-3500
-
Kirby R C and Logg A 2008 Benchmarking domain-specific compiler optimizations for variational forms ACM Trans. Math. Softw. 35 10
-
(2008)
ACM Trans. Math. Softw.
, vol.35
, Issue.2
, pp. 1
-
-
Kirby, R.C.1
Logg, A.2
-
447
-
-
79251522193
-
Unified embedded parallel finite element computations via software-based Fréchet differentiation
-
10.1137/09076920X 1064-8275
-
Long K, Kirby R and van Bloemen Waanders B 2010 Unified embedded parallel finite element computations via software-based Fréchet differentiation SIAM J. Sci. Comput. 32 3323-51
-
(2010)
SIAM J. Sci. Comput.
, vol.32
, Issue.6
, pp. 3323-3351
-
-
Long, K.1
Kirby, R.2
Van Bloemen Waanders, B.3
-
448
-
-
49749083442
-
Automated FEM discretizations for the Stokes equation
-
10.1007/s10543-008-0178-8 0006-3835
-
Terrel A R, Scott L R, Knepley M G and Kirby R C 2008 Automated FEM discretizations for the Stokes equation BIT Numer. Math. 48 389-404
-
(2008)
BIT Numer. Math.
, vol.48
, Issue.2
, pp. 389-404
-
-
Terrel, A.R.1
Scott, L.R.2
Knepley, M.G.3
Kirby, R.C.4
-
449
-
-
79952605821
-
From equations to code: Automated scientific computing
-
10.1109/MCSE.2011.31 1521-9615
-
Terrel A R 2011 From equations to code: automated scientific computing Comput. Sci. Eng. 13 78-82
-
(2011)
Comput. Sci. Eng.
, vol.13
, Issue.2
, pp. 78-82
-
-
Terrel, A.R.1
-
450
-
-
80052826347
-
A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations
-
10.1016/j.advwatres.2011.02.013 0309-1708
-
Mortensen M, Langtangen H P and Wells G N 2011 A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations Adv. Water Resources 34 1082-101
-
(2011)
Adv. Water Resources
, vol.34
, Issue.9
, pp. 1082-1101
-
-
Mortensen, M.1
Langtangen, H.P.2
Wells, G.N.3
-
451
-
-
57849101425
-
Automated code generation for discontinuous Galerkin methods
-
10.1137/070710032 1064-8275
-
Olgaard K B, Logg A and Wells G N 2008 Automated code generation for discontinuous Galerkin methods SIAM J. Sci. Comput. 31 849-64
-
(2008)
SIAM J. Sci. Comput.
, vol.31
, Issue.2
, pp. 849-864
-
-
Olgaard, K.B.1
Logg, A.2
Wells, G.N.3
|