-
1
-
-
77950792003
-
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm
-
McGuffee, S. R.; Elcock, A. H. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm PLoS Comput. Biol. 2010, 6, e1000694
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000694
-
-
McGuffee, S.R.1
Elcock, A.H.2
-
2
-
-
84871205477
-
A method for computing association rate constants of atomistically represented proteins under macromolecular crowding
-
Qin, S.; Cai, L.; Zhou, H.-X. A method for computing association rate constants of atomistically represented proteins under macromolecular crowding Phys. Biol. 2012, 9, 066008
-
(2012)
Phys. Biol.
, vol.9
, pp. 066008
-
-
Qin, S.1
Cai, L.2
Zhou, H.-X.3
-
3
-
-
84857128232
-
Protein-binding dynamics imaged in a living cell
-
Phillip, Y.; Kiss, V.; Schreiber, G. Protein-binding dynamics imaged in a living cell Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1461-1466
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 1461-1466
-
-
Phillip, Y.1
Kiss, V.2
Schreiber, G.3
-
4
-
-
68949143016
-
Common crowding agents have only a small effect on protein-protein interactions
-
Phillip, Y.; Sherman, E.; Haran, G.; Schreiber, G. Common crowding agents have only a small effect on protein-protein interactions Biophys. J. 2009, 97, 875-885
-
(2009)
Biophys. J.
, vol.97
, pp. 875-885
-
-
Phillip, Y.1
Sherman, E.2
Haran, G.3
Schreiber, G.4
-
5
-
-
44849122543
-
Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications
-
Lu, B. Z.; Zhou, Y. C.; Holst, M. J.; McCammon, J. A. Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications Comm. Comp. Phys. 2008, 3, 973-1009
-
(2008)
Comm. Comp. Phys.
, vol.3
, pp. 973-1009
-
-
Lu, B.Z.1
Zhou, Y.C.2
Holst, M.J.3
McCammon, J.A.4
-
6
-
-
20644431615
-
Theory of solutions of molecules containing widely separated charges with special application to zwitterions
-
Kirkwood, J. G. Theory of solutions of molecules containing widely separated charges with special application to zwitterions J. Chem. Phys. 1934, 2, 351-362
-
(1934)
J. Chem. Phys.
, vol.2
, pp. 351-362
-
-
Kirkwood, J.G.1
-
7
-
-
0009546303
-
Effects of intermacromolecular interactions on diffusion 0.1. 2-component solutions
-
Phillies, G. D. Effects of intermacromolecular interactions on diffusion 0.1. 2-component solutions J. Chem. Phys. 1974, 60, 976-982
-
(1974)
J. Chem. Phys.
, vol.60
, pp. 976-982
-
-
Phillies, G.D.1
-
8
-
-
0041971607
-
Effects of intermacromolecular interactions on diffusion 0.2. 3-component solutions
-
Phillies, G. D. Effects of intermacromolecular interactions on diffusion 0.2. 3-component solutions J. Chem. Phys. 1974, 60, 983-989
-
(1974)
J. Chem. Phys.
, vol.60
, pp. 983-989
-
-
Phillies, G.D.1
-
9
-
-
0032523702
-
Electrical double-layer interaction between heterogeneously charged colloidal particles: A superposition formulation
-
Sader, J. E.; Lenhoff, A. M. Electrical double-layer interaction between heterogeneously charged colloidal particles: a superposition formulation J. Colloid Interface Sci. 1998, 201, 233-243
-
(1998)
J. Colloid Interface Sci.
, vol.201
, pp. 233-243
-
-
Sader, J.E.1
Lenhoff, A.M.2
-
10
-
-
0032534446
-
The electrostatic interaction of rigid, globular proteins with arbitrary charge distributions
-
Mcclurg, R. B.; Zukoski, C. F. The electrostatic interaction of rigid, globular proteins with arbitrary charge distributions J. Colloid Interface Sci. 1998, 208, 529-542
-
(1998)
J. Colloid Interface Sci.
, vol.208
, pp. 529-542
-
-
McClurg, R.B.1
Zukoski, C.F.2
-
11
-
-
50249129675
-
An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis
-
Fenley, A. T.; Gordon, J. C.; Onufriev, A. An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis J. Chem. Phys. 2008, 129, 075101
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 075101
-
-
Fenley, A.T.1
Gordon, J.C.2
Onufriev, A.3
-
12
-
-
33846326929
-
An analytical electrostatic model for salt screened interactions between multiple proteins
-
Lotan, I.; Head-Gordon, T. An analytical electrostatic model for salt screened interactions between multiple proteins J. Chem. Theory Comput. 2006, 2, 541-555
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 541-555
-
-
Lotan, I.1
Head-Gordon, T.2
-
13
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
14
-
-
84986486656
-
A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls, A.; Honig, B. A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J. Comput. Chem. 1991, 12, 435-445
-
(1991)
J. Comput. Chem.
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
15
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions J. Phys. Chem. B 2001, 105, 6507-6514
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
16
-
-
44849142209
-
The finite element approximation of the nonlinear Poisson-Boltzmann equation
-
Chen, L.; Holst, M. J.; Xu, J. C. The finite element approximation of the nonlinear Poisson-Boltzmann equation Siam J. Numer. Anal. 2007, 45, 2298-2320
-
(2007)
Siam J. Numer. Anal.
, vol.45
, pp. 2298-2320
-
-
Chen, L.1
Holst, M.J.2
Xu, J.C.3
-
17
-
-
61549123719
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
-
Holst, M.; Baker, N.; Wang, F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples J. Comput. Chem. 2001, 22, 475-475
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 475-475
-
-
Holst, M.1
Baker, N.2
Wang, F.3
-
18
-
-
85033849708
-
Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy
-
Zhou, Z. X.; Payne, P.; Vasquez, M.; Kuhn, N.; Levitt, M. Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy J. Comput. Chem. 1996, 17, 1344-1351
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 1344-1351
-
-
Zhou, Z.X.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
-
19
-
-
65249120173
-
On removal of charge singularity in Poisson-Boltzmann equation
-
Cai, Q.; Wang, J.; Zhao, H.-K.; Luo, R. On removal of charge singularity in Poisson-Boltzmann equation J. Chem. Phys. 2009, 130, 145101
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 145101
-
-
Cai, Q.1
Wang, J.2
Zhao, H.-K.3
Luo, R.4
-
20
-
-
34648817162
-
Treatment of charge singularities in implicit solvent models
-
Geng, W.; Yu, S.; Wei, G. Treatment of charge singularities in implicit solvent models J. Chem. Phys. 2007, 127, 114106
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 114106
-
-
Geng, W.1
Yu, S.2
Wei, G.3
-
21
-
-
85033849708
-
Finite-difference solution of the Poisson-Boltzmann Equation: Complete elimination of self-energy
-
Zhou, Z.; Payne, P.; Vasquez, M.; Kuhn, N.; Levitt, M. Finite-difference solution of the Poisson-Boltzmann Equation: Complete elimination of self-energy J. Comput. Chem. 1996, 11, 1344-1351
-
(1996)
J. Comput. Chem.
, vol.11
, pp. 1344-1351
-
-
Zhou, Z.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
-
22
-
-
35348917599
-
Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities
-
Yu, S.; Wei, G. Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities J. Comput. Phys. 2007, 227, 602-632
-
(2007)
J. Comput. Phys.
, vol.227
, pp. 602-632
-
-
Yu, S.1
Wei, G.2
-
23
-
-
34248596727
-
Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
-
Yu, S.; Zhou, Y.; Wei, G. Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces J. Comput. Phys. 2007, 224, 729-756
-
(2007)
J. Comput. Phys.
, vol.224
, pp. 729-756
-
-
Yu, S.1
Zhou, Y.2
Wei, G.3
-
24
-
-
0001585447
-
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
-
Gilson, M. K.; Davis, M. E.; Luty, B. A.; McCammon, J. A. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation J. Chem. Phys. 1993, 97, 3591-3600
-
(1993)
J. Chem. Phys.
, vol.97
, pp. 3591-3600
-
-
Gilson, M.K.1
Davis, M.E.2
Luty, B.A.3
McCammon, J.A.4
-
25
-
-
0032096837
-
Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
-
Im, W.; Beglov, D.; Roux, B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput. Phys. Commun. 1998, 111, 59-75
-
(1998)
Comput. Phys. Commun.
, vol.111
, pp. 59-75
-
-
Im, W.1
Beglov, D.2
Roux, B.3
-
26
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis, M. E.; Mccammon, J. A. Electrostatics in biomolecular structure and dynamics Chem. Rev. 1990, 90, 509-521
-
(1990)
Chem. Rev.
, vol.90
, pp. 509-521
-
-
Davis, M.E.1
McCammon, J.A.2
-
27
-
-
0037328258
-
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
-
Bordner, A. J.; Huber, G. A. 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. 2003, 24, 353-367
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 353-367
-
-
Bordner, A.J.1
Huber, G.A.2
-
28
-
-
0037076079
-
Fast boundary element method for the linear Poisson-Boltzmann equation
-
Boschitsch, A. H.; Fenley, M. O.; Zhou, H. X. Fast boundary element method for the linear Poisson-Boltzmann equation J. Phys. Chem. B 2002, 106, 2741-2754
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 2741-2754
-
-
Boschitsch, A.H.1
Fenley, M.O.2
Zhou, H.X.3
-
29
-
-
0002334742
-
The electric-potential of a macromolecule in a solvent - A fundamental approach
-
Juffer, A. H.; Botta, E. F. F.; Vankeulen, B. A. M.; Vanderploeg, A.; Berendsen, H. J. C. The electric-potential of a macromolecule in a solvent-a fundamental approach J. Comput. Phys. 1991, 97, 144-171
-
(1991)
J. Comput. Phys.
, vol.97
, pp. 144-171
-
-
Juffer, A.H.1
Botta, E.F.F.2
Vankeulen, B.A.M.3
Vanderploeg, A.4
Berendsen, H.J.C.5
-
30
-
-
0022429751
-
A new method for computing the macromolecular electric-potential
-
Zauhar, R. J.; Morgan, R. S. A new method for computing the macromolecular electric-potential J. Mol. Biol. 1985, 186, 815-820
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 815-820
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
31
-
-
0027254625
-
Boundary-element solution of macromolecular electrostatics - Interaction energy between 2 proteins
-
Zhou, H. X. Boundary-element solution of macromolecular electrostatics-interaction energy between 2 proteins Biophys. J. 1993, 65, 955-963
-
(1993)
Biophys. J.
, vol.65
, pp. 955-963
-
-
Zhou, H.X.1
-
32
-
-
34548772137
-
Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations
-
Lu, B. Z.; McCammon, J. A. Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations J. Chem. Theory Comput. 2007, 3, 1134-1142
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1134-1142
-
-
Lu, B.Z.1
McCammon, J.A.2
-
33
-
-
77950630374
-
AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
-
Lu, B.; Cheng, X.; Huang, J.; McCammon, J. A. AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems Comput. Phys. Commun. 2010, 181, 1150-1160
-
(2010)
Comput. Phys. Commun.
, vol.181
, pp. 1150-1160
-
-
Lu, B.1
Cheng, X.2
Huang, J.3
McCammon, J.A.4
-
34
-
-
79251630269
-
A new and efficient Poisson-Boltzmann solver for interaction of multiple proteins
-
Yap, E.-H.; Head-Gordon, T. A new and efficient Poisson-Boltzmann solver for interaction of multiple proteins J. Chem. Theory Comput. 2010, 6, 2214-2224
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2214-2224
-
-
Yap, E.-H.1
Head-Gordon, T.2
-
35
-
-
0029873697
-
Rapid, electrostatically assisted association of proteins
-
Schreiber, G.; Fersht, A. R. Rapid, electrostatically assisted association of proteins Nat. Struct. Biol. 1996, 3, 427-431
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 427-431
-
-
Schreiber, G.1
Fersht, A.R.2
-
36
-
-
0030891436
-
Simulation of the diffusional association of Barnase and Barstar
-
Gabdoulline, R. R.; Wade, R. C. Simulation of the diffusional association of Barnase and Barstar Biophys. J. 1997, 72, 1917-1929
-
(1997)
Biophys. J.
, vol.72
, pp. 1917-1929
-
-
Gabdoulline, R.R.1
Wade, R.C.2
-
38
-
-
36549102274
-
Brownian dynamics simulation of diffusion-influenced bimolecular reactions
-
Northrup, S.; Allison, S.; McCammon, J. A. Brownian dynamics simulation of diffusion-influenced bimolecular reactions J. Chem. Phys. 1984, 80, 1517-1524
-
(1984)
J. Chem. Phys.
, vol.80
, pp. 1517-1524
-
-
Northrup, S.1
Allison, S.2
McCammon, J.A.3
-
39
-
-
0001447029
-
Minimal discrete energy on the sphere
-
Rakhmanov, E.; Saff, E.; Zhou, Y. Minimal discrete energy on the sphere Math. Res. Lett. 1994, 1, 647-662
-
(1994)
Math. Res. Lett.
, vol.1
, pp. 647-662
-
-
Rakhmanov, E.1
Saff, E.2
Zhou, Y.3
-
40
-
-
33750652614
-
Brownian dynamics with hydrodynamic interactions
-
Ermak, D. L.; McCammon, J. A. Brownian dynamics with hydrodynamic interactions J. Chem. Phys. 1978, 69, 1352-1360
-
(1978)
J. Chem. Phys.
, vol.69
, pp. 1352-1360
-
-
Ermak, D.L.1
McCammon, J.A.2
-
41
-
-
0028074974
-
Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-A resolution
-
Buckle, A. M.; Schreiber, G.; Fersht, A. R. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution Biochemistry 1994, 33, 8878-8889
-
(1994)
Biochemistry
, vol.33
, pp. 8878-8889
-
-
Buckle, A.M.1
Schreiber, G.2
Fersht, A.R.3
-
42
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 1998, 11, 739-747
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
43
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 2007, 35, W522-W525
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
44
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 2004, 32, W665-W667
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
45
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J. M.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
46
-
-
28644432877
-
Very fast empirical prediction and interpretation of protein pKa values
-
Li, H.; Robertson, A. D.; Jensen, J. H. Very fast empirical prediction and interpretation of protein pKa values Proteins 2005, 61, 704-721
-
(2005)
Proteins
, vol.61
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
47
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner, M. F.; Olson, A. J.; Spehner, J. C. Reduced surface: An efficient way to compute molecular surfaces Biopolymers 1996, 38, 305-320
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
|