-
1
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
Feig, M.; Brooks, C. L., III. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
2
-
-
17044392602
-
Improving implicit solvent simulations: A Poisson-centric view
-
Baker, N. A. Improving implicit solvent simulations: a Poisson-centric view. Curr. Opin. Struct. Biol. 2005, 15 (2), 137-143.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, Issue.2
, pp. 137-143
-
-
Baker, N.A.1
-
3
-
-
0032968133
-
Implicit Solvent, Models
-
Roux, B.; Simonson, T. Implicit Solvent, Models. Biophys. Chem. 1999, 78, 1-20.
-
(1999)
Biophys. Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
4
-
-
84961981091
-
Implicit solvation models: Equilibria, structure spectra and dynamics
-
Cramer, C. J.; Truhlar, D. G. Implicit solvation models: Equilibria, structure spectra and dynamics. Chem. Rev. 1999, 99, 2161-2200.
-
(1999)
Chem. Rev
, vol.99
, pp. 2161-2200
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
5
-
-
32844457567
-
Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
6
-
-
0029016182
-
Classical Electrostatics in Biology and Chemistry
-
Honig, B.; Nicholls, A. Classical Electrostatics in Biology and Chemistry. Science 1995, 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
7
-
-
0025283002
-
Electrostatic Interactions in Macromolecules - Theory and Applications
-
Sharp, K. A.; Honig, B. Electrostatic Interactions in Macromolecules - Theory and Applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
8
-
-
0020475509
-
Calculation of the Electric Potentialin the Active Site Cleft due to α-Helix Dipoles
-
Warwicker, J.; Watson, H. C. Calculation of the Electric Potentialin the Active Site Cleft due to α-Helix Dipoles. J. Mol. Biol. 1982, 157, 671-679.
-
(1982)
J. Mol. Biol
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
9
-
-
0036873086
-
The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology
-
Fogolari, F.; Brigo, A.; Molinari, H. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J. Mol. Recognit. 2002, 15, 377-392.
-
(2002)
J. Mol. Recognit
, vol.15
, pp. 377-392
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
10
-
-
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
-
11
-
-
0000779818
-
Poisson-Boltzmann analytical gradients for molecular modeling calculations
-
Friedrichs, M.; Zhou, R. H.; Edinger, S. R.; Friesner, R. A. Poisson-Boltzmann analytical gradients for molecular modeling calculations. J. Phys. Chem. B 1999, 103, 3057-3061.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3057-3061
-
-
Friedrichs, M.1
Zhou, R.H.2
Edinger, S.R.3
Friesner, R.A.4
-
12
-
-
0037103014
-
Protein Molecular Dynamics With Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation
-
Lu, B. Z.; Chen, W. Z.; Wang, C. X.; Xu, X.-j. Protein Molecular Dynamics With Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation. Proteins 2002, 48, 497-504.
-
(2002)
Proteins
, vol.48
, pp. 497-504
-
-
Lu, B.Z.1
Chen, W.Z.2
Wang, C.X.3
Xu, X.-J.4
-
13
-
-
0036771626
-
Accelerated Poisson-Boltzmann Calculations for Static and Dynamic Systems
-
Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann Calculations for Static and Dynamic Systems. J. Comput. Chem. 2002, 23, 1244-1253.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
14
-
-
0344778061
-
Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics
-
Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
15
-
-
33644792311
-
What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules
-
Yu, Z. Y.; Jacobson, M. P.; Friesner, R. A. What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules. J. Comput. Chem. 2006, 27 (1), 72-89.
-
(2006)
J. Comput. Chem
, vol.27
, Issue.1
, pp. 72-89
-
-
Yu, Z.Y.1
Jacobson, M.P.2
Friesner, R.A.3
-
16
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004, 55 (2), 383-394.
-
(2004)
Proteins
, vol.55
, Issue.2
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
17
-
-
0346971105
-
Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures
-
Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A. Brooks, C. L., III. Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures. J. Comput. Chem. 2004, 25, 265-284.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
-
18
-
-
0141453063
-
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
-
Grycuk, T. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation. J. Chem. Phys. 2003, 119, 4817-4826.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 4817-4826
-
-
Grycuk, T.1
-
19
-
-
0347602124
-
Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf
-
Gohlke, H.; Case, D. A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf. J. Comput. Chem. 2003, 25, 238-250.
-
(2003)
J. Comput. Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
20
-
-
0037157693
-
Novel generalized Born methods
-
24
-
Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. Novel generalized Born methods. J. Chem Phys. 2002, 116 (24), 10606-10614.
-
(2002)
J. Chem Phys
, vol.116
, pp. 10606-10614
-
-
Lee, M.S.1
Salsbury Jr., F.R.2
Brooks III, C.L.3
-
21
-
-
1442330396
-
An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling
-
Gallicchio, E.; Levy, R. M. AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling. J. Comput. Chem. 2004, 25, 479-499.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 479-499
-
-
Gallicchio, E.1
Levy, R.2
AGBNP, M.3
-
22
-
-
12344297201
-
Generalized Langevin Theory for Many-Body Problems in Chemical-Dynamics - Gas-Surface Collisions Vibrational-Energy Relaxation in Solids and Recombination Reactions in Liquids
-
Brooks, C. L.; Berkowitz, M.; Adelman, S. A. Generalized Langevin Theory for Many-Body Problems in Chemical-Dynamics - Gas-Surface Collisions Vibrational-Energy Relaxation in Solids and Recombination Reactions in Liquids. J. Chem. Phys. 1980, 73 (9), 4353-4364.
-
(1980)
J. Chem. Phys
, vol.73
, Issue.9
, pp. 4353-4364
-
-
Brooks, C.L.1
Berkowitz, M.2
Adelman, S.A.3
-
23
-
-
0042561888
-
Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study
-
Zagrovic, B.; Pande, V. Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study. J. Comput. Chem. 2003, 24, 1432-1436.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1432-1436
-
-
Zagrovic, B.1
Pande, V.2
-
24
-
-
0347526155
-
Time-reversible deterministic thermostats
-
Hoover, W. G.; Aoki, K.; Hoover, C. G.; De Groot, S. V. Time-reversible deterministic thermostats. Physica D 2004, 187 (1-4), 253-267.
-
(2004)
Physica D
, vol.187
, Issue.1-4
, pp. 253-267
-
-
Hoover, W.G.1
Aoki, K.2
Hoover, C.G.3
De Groot, S.V.4
-
25
-
-
84943502952
-
-
Nose, S. A Molecular Dynamics Method for Simulations in the Canonical Ensemble. Mol. Phys. 1984, 52, 255-268.
-
Nose, S. A Molecular Dynamics Method for Simulations in the Canonical Ensemble. Mol. Phys. 1984, 52, 255-268.
-
-
-
-
26
-
-
33646645973
-
Constant-Pressure Equations of Motion
-
Hoover, W. G. Constant-Pressure Equations of Motion. Phys. Rev. A: At., Mol., Opt. Phys. 1986, 34 (3), 2499-2500.
-
(1986)
Phys. Rev. A: At., Mol., Opt. Phys
, vol.34
, Issue.3
, pp. 2499-2500
-
-
Hoover, W.G.1
-
27
-
-
0035850758
-
β-Hairpin Folding Simulations in Atomistic Detail Using an Implicit Solvent Model
-
Zagrovic, B.; Sorin, E. J.; Pande, V. β-Hairpin Folding Simulations in Atomistic Detail Using an Implicit Solvent Model. J. Mol. Biol. 2001, 313, 151-169.
-
(2001)
J. Mol. Biol
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
-
28
-
-
18744382161
-
Comparative study of generalized Born models: Protein dynamics
-
Fan, H.; Mark, A. E.; Zhu, J.; Honig, B. Comparative study of generalized Born models: Protein dynamics. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (19), 6760-6764.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.19
, pp. 6760-6764
-
-
Fan, H.1
Mark, A.E.2
Zhu, J.3
Honig, B.4
-
29
-
-
0042139644
-
Comparison of Generalized Born and Poisson Models: Energetics and Dynamics of HIV Protease
-
David, L.; Luo, R.; Gilson, M. K. Comparison of Generalized Born and Poisson Models: Energetics and Dynamics of HIV Protease. J. Comput. Chem. 2000, 21, 295-309.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 295-309
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
30
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids with a generalized Born solvation model
-
Tsui, V.; Case, D. A. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 2000, 122, 2489-2498.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
31
-
-
0035501755
-
Protein Molecular Dynamics With the Generalized Born/ACE Solvent Model
-
Calimet, N.; Schaefer, M.; Simonson, T. Protein Molecular Dynamics With the Generalized Born/ACE Solvent Model. Proteins 2001, 45, 144-158.
-
(2001)
Proteins
, vol.45
, pp. 144-158
-
-
Calimet, N.1
Schaefer, M.2
Simonson, T.3
-
32
-
-
0036138028
-
Evaluation of a Fast Implicit Solvent Model for Molecular Dynamics Simulations
-
Ferrara, P.; Apostolakis, J.; Caflish, A. Evaluation of a Fast Implicit Solvent Model for Molecular Dynamics Simulations. Proteins 2002, 46, 24-33.
-
(2002)
Proteins
, vol.46
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflish, A.3
-
33
-
-
0041375556
-
Replica-exchange, molecular dynamics simulations for a small-sized protein folding with implicit solvent
-
Suenaga, A. Replica-exchange, molecular dynamics simulations for a small-sized protein folding with implicit solvent. THEOCHEM 2003, 634, 235-241.
-
(2003)
THEOCHEM
, vol.634
, pp. 235-241
-
-
Suenaga, A.1
-
34
-
-
0036217783
-
-
Shen, M.-y.; Freed, K. F. Long Time Dynamics of Met-Enkephalin: Comparison of Explicit and Implicit Solvent Models. Biophys. J. 2002, 82, 1791-1808.
-
Shen, M.-y.; Freed, K. F. Long Time Dynamics of Met-Enkephalin: Comparison of Explicit and Implicit Solvent Models. Biophys. J. 2002, 82, 1791-1808.
-
-
-
-
35
-
-
0141677983
-
Comparison of Various Implicit Solvent Models in Molecular Dynamics Simulations of Immunoglobulin G Light Chain Dimer
-
Krol, M. Comparison of Various Implicit Solvent Models in Molecular Dynamics Simulations of Immunoglobulin G Light Chain Dimer. J. Comput. Chem. 2003, 24, 531-546.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 531-546
-
-
Krol, M.1
-
36
-
-
0034510764
-
Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models
-
Bursulaya, B. D.; Brooks, C. L., III. 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 2000, 104 (51), 12378-12383.
-
(2000)
J. Phys. Chem. B
, vol.104
, Issue.51
, pp. 12378-12383
-
-
Bursulaya, B.D.1
Brooks III, C.L.2
-
37
-
-
33748774659
-
Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment
-
Chocholousova, J.; Feig, M. Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment. J. Phys. Chem. B 2006, 110 (34), 17240-17251.
-
(2006)
J. Phys. Chem. B
, vol.110
, Issue.34
, pp. 17240-17251
-
-
Chocholousova, J.1
Feig, M.2
-
38
-
-
33645703426
-
Balancing an Accurate Representation of the Molecular Surface in Generalized Born Formalisms with Integrator Stability in Molecular Dynamics Simulations
-
Chocholousova, J.; Feig, M. Balancing an Accurate Representation of the Molecular Surface in Generalized Born Formalisms with Integrator Stability in Molecular Dynamics Simulations. J. Comput. Chem 2006, 27, 719-729.
-
(2006)
J. Comput. Chem
, vol.27
, pp. 719-729
-
-
Chocholousova, J.1
Feig, M.2
-
39
-
-
14544285906
-
Comparativestudy of generalized Born models: Born radii and peptide folding
-
Zhu, J.; Alexov, E.; Honig, B. Comparativestudy of generalized Born models: Born radii and peptide folding. J. Phys. Chem. B 2005, 109 (7), 3008-3022.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.7
, pp. 3008-3022
-
-
Zhu, J.1
Alexov, E.2
Honig, B.3
-
40
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field
-
Chen, J. H.; Im, W. P.; Brooks, C. L. Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field. J. Am. Chem. Soc. 2006, 128 (11), 3728-3736.
-
(2006)
J. Am. Chem. Soc
, vol.128
, Issue.11
, pp. 3728-3736
-
-
Chen, J.H.1
Im, W.P.2
Brooks, C.L.3
-
41
-
-
33745960026
-
Investigation of salt bridge stability in a generalized born solvent model
-
Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C. Investigation of salt bridge stability in a generalized born solvent model. J. Chem. Theory Comput. 2006, 2 (1), 115-127.
-
(2006)
J. Chem. Theory Comput
, vol.2
, Issue.1
, pp. 115-127
-
-
Geney, R.1
Layten, M.2
Gomperts, R.3
Hornak, V.4
Simmerling, C.5
-
42
-
-
0037046727
-
Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics
-
Zhu, J.; Shi, Y.; Liu, H. Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics. J. Phys. Chem. B 2002, 106, 4844-4853.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 4844-4853
-
-
Zhu, J.1
Shi, Y.2
Liu, H.3
-
43
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Nymeyer, H.; Garcia, A. E. Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13934-13939.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
44
-
-
0033577269
-
Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration
-
Kuszewski, J.; Gronenborn, A. M.; Clore, G. M. Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration. J. Am. Chem. Soc. 1999, 121, 2337-2338.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 2337-2338
-
-
Kuszewski, J.1
Gronenborn, A.M.2
Clore, G.M.3
-
45
-
-
0032528033
-
Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase
-
Cornilescu, G.; Marquardt, J. L.; Ottiger, M.; Bax, A. Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase. J. Am. Chem. Soc. 1998, 120, 6836-6837.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 6836-6837
-
-
Cornilescu, G.1
Marquardt, J.L.2
Ottiger, M.3
Bax, A.4
-
46
-
-
0041784950
-
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, J. D.; Evanseck, M. J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattes, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, J. D.; Evanseck, M. J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattes, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
-
-
-
47
-
-
3142714765
-
-
MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400-1415.
-
MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400-1415.
-
-
-
-
48
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 2004, 126, 698-699.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 698-699
-
-
MacKerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
49
-
-
33646940952
-
Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23 (3), 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
50
-
-
0038792211
-
New Analytical Approximation to the Standard Molecular Volume Definition And Its Application to Generalized BornCalculations
-
Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. New Analytical Approximation to the Standard Molecular Volume Definition And Its Application to Generalized BornCalculations. J. Comput. Chem. 2003, 24, 1348-1356.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury Jr., F.R.3
Brooks III, C.L.4
-
51
-
-
0141956090
-
Generalized Born model with a simple smoothing function
-
Im, W.; Lee, M. S.; Brooks, C. L., III. Generalized Born model with a simple smoothing function. J. Comput. Chem. 2003, 24, 1691-1702.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
52
-
-
84986512474
-
CHARMM: A Program for Macromolecular Energy Minimization and Dynamics Calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy Minimization and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, 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
-
53
-
-
1942423619
-
MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology
-
Feig, M.; Karanicolas, J.; Brooks, C. L., III. MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology. J. Mol. Graphics Modell. 2004, 22, 377-395.
-
(2004)
J. Mol. Graphics Modell
, vol.22
, pp. 377-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks III, C.L.3
-
54
-
-
0038054912
-
Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations
-
Feig, M.; MacKerell, A. D.; Brooks, C. L. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B 2003, 107 (12), 2831-2836.
-
(2003)
J. Phys. Chem. B
, vol.107
, Issue.12
, pp. 2831-2836
-
-
Feig, M.1
MacKerell, A.D.2
Brooks, C.L.3
-
56
-
-
0000279972
-
Influence of Vibrational Motion on Solid-State Line-Shapes and Nmr Relaxation
-
Henry, E. R.; Szabo, A. Influence of Vibrational Motion on Solid-State Line-Shapes and Nmr Relaxation. J. Chem. Phys. 1985, 82 (11), 4753-4761.
-
(1985)
J. Chem. Phys
, vol.82
, Issue.11
, pp. 4753-4761
-
-
Henry, E.R.1
Szabo, A.2
-
57
-
-
0028354429
-
2 Crystal-Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein-G and Comparison with Nmr
-
Gallagher, T.; Alexander, P.; Bryan, P.; Gilliland, G. L. 2 Crystal-Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein-G and Comparison with Nmr. Biochemistry 1994, 33 (15), 4721-4729.
-
(1994)
Biochemistry
, vol.33
, Issue.15
, pp. 4721-4729
-
-
Gallagher, T.1
Alexander, P.2
Bryan, P.3
Gilliland, G.L.4
-
58
-
-
0023644679
-
Structure of Ubiquitin Refined at 1.8 a Resolution
-
Vijaykumar, S.; Bugg, C. E.; Cook, W. J. Structure of Ubiquitin Refined at 1.8 a Resolution. J. Mol. Biol. 1987, 194 (3), 531-544.
-
(1987)
J. Mol. Biol
, vol.194
, Issue.3
, pp. 531-544
-
-
Vijaykumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
59
-
-
0028230020
-
Synthetic Structural and Biological Studies of the Ubiquitin System - Chemically Synthesized and Native Ubiquitin Fold into Identical 3-Dimensional Structures
-
Alexeev, D.; Bury, S. M.; Turner, M. A.; Ogunjobi, O. M.; Muir, T. W.; Ramage, R.; Sawyer, L. Synthetic Structural and Biological Studies of the Ubiquitin System - Chemically Synthesized and Native Ubiquitin Fold into Identical 3-Dimensional Structures. Biochem. J. 1994, 299, 159-163.
-
(1994)
Biochem. J
, vol.299
, pp. 159-163
-
-
Alexeev, D.1
Bury, S.M.2
Turner, M.A.3
Ogunjobi, O.M.4
Muir, T.W.5
Ramage, R.6
Sawyer, L.7
-
60
-
-
33646719091
-
Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance Relaxation in Macromolecules. 1. Theory and Range of Validity
-
Lipari, G.; Szabo, A. Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance Relaxation in Macromolecules. 1. Theory and Range of Validity. J. Am. Chem. Soc. 1982, 104 (17), 4546-4559.
-
(1982)
J. Am. Chem. Soc
, vol.104
, Issue.17
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
61
-
-
33845553743
-
Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance Relaxation in Macromolecules. 2. Analysis of Experimental Results
-
Lipari, G.; Szabo, A. Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance Relaxation in Macromolecules. 2. Analysis of Experimental Results. J. Am. Chem. Soc. 1982, 104 (17), 4559-4570.
-
(1982)
J. Am. Chem. Soc
, vol.104
, Issue.17
, pp. 4559-4570
-
-
Lipari, G.1
Szabo, A.2
-
62
-
-
0026869597
-
Langevin Dynamics of Peptides - the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N′-Methylamide
-
Loncharich, R. J.; Brooks, B. R.; Pastor, R. W. Langevin Dynamics of Peptides - the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N′-Methylamide. Biopolymers 1992, 32 (5), 523-535.
-
(1992)
Biopolymers
, vol.32
, Issue.5
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
63
-
-
24144469761
-
Diffusional limits to the speed of protein folding: Fact or friction?
-
Hagen, S. J.; Qiu, L. L.; Pabit, S. A. Diffusional limits to the speed of protein folding: fact or friction? J. Phys.: Condens. Matter. 2005, 17 (18), S1503-S1514.
-
(2005)
J. Phys.: Condens. Matter
, vol.17
, Issue.18
-
-
Hagen, S.J.1
Qiu, L.L.2
Pabit, S.A.3
-
64
-
-
29344442281
-
Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer
-
Gee, P. J.; van Gunsteren, W. F. Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer. Chem. - Eur. J. 2005, 12 (1), 72-75.
-
(2005)
Chem. - Eur. J
, vol.12
, Issue.1
, pp. 72-75
-
-
Gee, P.J.1
van Gunsteren, W.F.2
-
65
-
-
33947723327
-
Influence of Temperature Friction and Random Forces on Folding of the B-Domain of Staphylococcal Protein A: All-Atom Molecular Dynamics in Implicit Solvent
-
Jagielska, A.; Scheraga, H. A. Influence of Temperature Friction and Random Forces on Folding of the B-Domain of Staphylococcal Protein A: All-Atom Molecular Dynamics in Implicit Solvent. J. Comput. Chem. 2007, 28, 1068-1082.
-
(2007)
J. Comput. Chem
, vol.28
, pp. 1068-1082
-
-
Jagielska, A.1
Scheraga, H.A.2
-
66
-
-
10944260594
-
Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous, and discrete-state kinetic models
-
Chekmarev, D. S.; Ishida, T.; Levy, R. M. Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous, and discrete-state kinetic models. J. Phys. Chem. B 2004, 108 (50), 19487-19495.
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.50
, pp. 19487-19495
-
-
Chekmarev, D.S.1
Ishida, T.2
Levy, R.M.3
-
67
-
-
2942567954
-
Describing protein folding kinetics by molecular dynamics simulations. 1. Theory
-
Swope, W. C.; Pitera, J. W.; Suits, F. Describing protein folding kinetics by molecular dynamics simulations. 1. Theory. J. Phys. Chem. B 2004, 108 (21), 6571-6581.
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.21
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
68
-
-
2942560604
-
Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and beta-hairpin peptide
-
Swope, W. C.; Pitera, J. W.; Suits, F.; Pitman, M.; Eleftheriou, M.; Fitch, B. G.; Germain, R. S.; Rayshubski, A.; Ward, T. J. C.; Zhestkov, Y.; Zhou, R. Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and beta-hairpin peptide. J. Phys. Chem. B 2004, 108 (21), 6582-6594.
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.21
, pp. 6582-6594
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
Pitman, M.4
Eleftheriou, M.5
Fitch, B.G.6
Germain, R.S.7
Rayshubski, A.8
Ward, T.J.C.9
Zhestkov, Y.10
Zhou, R.11
-
69
-
-
0029878720
-
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graphics 1996, 14 (1), 33.
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graphics 1996, 14 (1), 33.
-
-
-
-
70
-
-
0033577269
-
Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration
-
Kuszewski, J.; Gronenborn, A. M.; Clore, G. M. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J. Am. Chem. Soc. 1999, 121 (10), 2337-2338.
-
(1999)
J. Am. Chem. Soc
, vol.121
, Issue.10
, pp. 2337-2338
-
-
Kuszewski, J.1
Gronenborn, A.M.2
Clore, G.M.3
-
71
-
-
0038062647
-
(NH)-N-15 backbone dynamics of protein GB1: Comparison of order parameters and correlation times derived using various "model-free" approaches
-
Idiyatullin, D.; Daragan, V. A.; Mayo, K. H. (NH)-N-15 backbone dynamics of protein GB1: Comparison of order parameters and correlation times derived using various "model-free" approaches. J. Phys. Chem. B 2003, 107 (11), 2602-2609.
-
(2003)
J. Phys. Chem. B
, vol.107
, Issue.11
, pp. 2602-2609
-
-
Idiyatullin, D.1
Daragan, V.A.2
Mayo, K.H.3
-
72
-
-
0032528033
-
Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
-
Cornilescu, G.; Marquardt, J. L.; Ottiger, M.; Bax, A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 1998, 120 (27), 6836-6837.
-
(1998)
J. Am. Chem. Soc
, vol.120
, Issue.27
, pp. 6836-6837
-
-
Cornilescu, G.1
Marquardt, J.L.2
Ottiger, M.3
Bax, A.4
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