메뉴 건너뛰기




Volumn 16, Issue 2, 2006, Pages 142-151

Electrostatics calculations: latest methodological advances

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT;

EID: 33645981305     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2006.03.001     Document Type: Review
Times cited : (190)

References (87)
  • 1
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 14 (1959) 1-63
    • (1959) Adv Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 2
    • 0018094892 scopus 로고
    • Electrostatic effects in proteins
    • Perutz M.F. Electrostatic effects in proteins. Science 201 (1978) 1187-1191
    • (1978) Science , vol.201 , pp. 1187-1191
    • Perutz, M.F.1
  • 3
    • 1542440402 scopus 로고    scopus 로고
    • Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules-applications in biotechnology
    • Neves-Petersen M.T., and Petersen S.B. Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules-applications in biotechnology. Biotechnol Annu Rev 9 (2003) 315-395
    • (2003) Biotechnol Annu Rev , vol.9 , pp. 315-395
    • Neves-Petersen, M.T.1    Petersen, S.B.2
  • 4
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized Born solvation model in macromolecular simulations
    • Tsui V., and Case D.A. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56 (2000) 275-291
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 5
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D., and Case D.A. Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 51 (2000) 129-152
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 6
    • 0035312551 scopus 로고    scopus 로고
    • Macromolecular electrostatics: continuum models and their growing pains
    • Simonson T. Macromolecular electrostatics: continuum models and their growing pains. Curr Opin Struct Biol 11 (2001) 243-252
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 243-252
    • Simonson, T.1
  • 7
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig M., and Brooks III C.L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol 14 (2004) 217-224
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 8
    • 1642464809 scopus 로고    scopus 로고
    • Poisson-Boltzmann methods for biomolecular electrostatics
    • Baker N.A. Poisson-Boltzmann methods for biomolecular electrostatics. Methods Enzymol 383 (2004) 94-118
    • (2004) Methods Enzymol , vol.383 , pp. 94-118
    • Baker, N.A.1
  • 9
    • 17044392602 scopus 로고    scopus 로고
    • Improving implicit solvent simulations: a Poisson-centric view
    • This review of implicit solvent models surveys recent methodological advances in solving the PB equation.
    • Baker N.A. Improving implicit solvent simulations: a Poisson-centric view. Curr Opin Struct Biol 15 (2005) 137-143. This review of implicit solvent models surveys recent methodological advances in solving the PB equation.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 137-143
    • Baker, N.A.1
  • 10
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules: long-range electrostatic effects
    • Sagui C., and Darden T.A. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct 28 (1999) 155-179
    • (1999) Annu Rev Biophys Biomol Struct , vol.28 , pp. 155-179
    • Sagui, C.1    Darden, T.A.2
  • 11
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder J.W., and Case D.A. Force fields for protein simulations. Adv Protein Chem 66 (2003) 27-85
    • (2003) Adv Protein Chem , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 12
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: overview and issues
    • Mackerell Jr. A.D. Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25 (2004) 1584-1604
    • (2004) J Comput Chem , vol.25 , pp. 1584-1604
    • Mackerell Jr., A.D.1
  • 13
    • 0035312897 scopus 로고    scopus 로고
    • Electrostatics calculations: recent methodological advances and applications to membranes
    • Tobias D.J. Electrostatics calculations: recent methodological advances and applications to membranes. Curr Opin Struct Biol 11 (2001) 253-261
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 253-261
    • Tobias, D.J.1
  • 14
    • 29944444169 scopus 로고    scopus 로고
    • Implicit solvent simulation models for biomembranes
    • This review of implicit solvent models focuses on calculations relevant to membrane systems. It surveys coarse-grained representations of membranes and describes simulation techniques adapted to these approximate representations, in which the solvent is considered implicitly.
    • Brannigan G., Lin L.C., and Brown F.L. Implicit solvent simulation models for biomembranes. Eur Biophys J 35 (2005) 104-124. This review of implicit solvent models focuses on calculations relevant to membrane systems. It surveys coarse-grained representations of membranes and describes simulation techniques adapted to these approximate representations, in which the solvent is considered implicitly.
    • (2005) Eur Biophys J , vol.35 , pp. 104-124
    • Brannigan, G.1    Lin, L.C.2    Brown, F.L.3
  • 15
    • 0034426864 scopus 로고    scopus 로고
    • Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association
    • Gibas C.J., Jambeck P., and Subramaniam S. Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association. Methods 20 (2000) 292-309
    • (2000) Methods , vol.20 , pp. 292-309
    • Gibas, C.J.1    Jambeck, P.2    Subramaniam, S.3
  • 16
    • 0034039797 scopus 로고    scopus 로고
    • Electrostatic aspects of protein-protein interactions
    • Sheinerman F.B., Norel R., and Honig B. Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol 10 (2000) 153-159
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 153-159
    • Sheinerman, F.B.1    Norel, R.2    Honig, B.3
  • 17
    • 0034979318 scopus 로고    scopus 로고
    • Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
    • Wang W., Donini O., Reyes C.M., and Kollman P.A. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 30 (2001) 211-243
    • (2001) Annu Rev Biophys Biomol Struct , vol.30 , pp. 211-243
    • Wang, W.1    Donini, O.2    Reyes, C.M.3    Kollman, P.A.4
  • 18
    • 0036890316 scopus 로고    scopus 로고
    • Electrostatics in protein binding and function
    • Sinha N., and Smith-Gill S.J. Electrostatics in protein binding and function. Curr Protein Pept Sci 3 (2002) 601-614
    • (2002) Curr Protein Pept Sci , vol.3 , pp. 601-614
    • Sinha, N.1    Smith-Gill, S.J.2
  • 19
    • 27744498365 scopus 로고    scopus 로고
    • Electrostatics in computational protein design
    • The complexity and computational cost of in silico protein design have led to the development of many approximate methods for computing electrostatics, focusing on pairwise decomposable models. These methods are reviewed in this paper, with emphasis on implicit solvent models.
    • Vizcarra C.L., and Mayo S.L. Electrostatics in computational protein design. Curr Opin Chem Biol 9 (2005) 622-626. The complexity and computational cost of in silico protein design have led to the development of many approximate methods for computing electrostatics, focusing on pairwise decomposable models. These methods are reviewed in this paper, with emphasis on implicit solvent models.
    • (2005) Curr Opin Chem Biol , vol.9 , pp. 622-626
    • Vizcarra, C.L.1    Mayo, S.L.2
  • 20
    • 0036902235 scopus 로고    scopus 로고
    • Close-range electrostatic interactions in proteins
    • Kumar S., and Nussinov R. Close-range electrostatic interactions in proteins. ChemBioChem 3 (2002) 604-617
    • (2002) ChemBioChem , vol.3 , pp. 604-617
    • Kumar, S.1    Nussinov, R.2
  • 21
    • 4043175563 scopus 로고    scopus 로고
    • Different roles of electrostatics in heat and in cold: adaptation by citrate synthase
    • Kumar S., and Nussinov R. Different roles of electrostatics in heat and in cold: adaptation by citrate synthase. ChemBioChem 5 (2004) 280-290
    • (2004) ChemBioChem , vol.5 , pp. 280-290
    • Kumar, S.1    Nussinov, R.2
  • 22
    • 20344368593 scopus 로고    scopus 로고
    • A quantum mechanical polarizable force field for biomolecular interactions
    • This paper introduces a quantum mechanical polarizable force-field that is optimized for drug design. It is shown to agree well with experimental data in simulations of methane and methanol in gas phases. This force-field was developed with the simulation of large biomolecular systems in mind.
    • Donchev A.G., Ozrin V.D., Subbotin M.V., Tarasov O.V., and Tarasov V.I. A quantum mechanical polarizable force field for biomolecular interactions. Proc Natl Acad Sci USA 102 (2005) 7829-7834. This paper introduces a quantum mechanical polarizable force-field that is optimized for drug design. It is shown to agree well with experimental data in simulations of methane and methanol in gas phases. This force-field was developed with the simulation of large biomolecular systems in mind.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7829-7834
    • Donchev, A.G.1    Ozrin, V.D.2    Subbotin, M.V.3    Tarasov, O.V.4    Tarasov, V.I.5
  • 23
    • 18744378855 scopus 로고    scopus 로고
    • Ab initio quantum chemistry: methodology and applications
    • This perspective article provides an overview of the state of the art in ab initio quantum chemical methodology and applications.
    • Friesner R.A. Ab initio quantum chemistry: methodology and applications. Proc Natl Acad Sci USA 102 (2005) 6648-6653. This perspective article provides an overview of the state of the art in ab initio quantum chemical methodology and applications.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6648-6653
    • Friesner, R.A.1
  • 24
    • 27344454932 scopus 로고    scopus 로고
    • GROMACS: fast, flexible, and free
    • This paper presents an overview of the GROMACS package for molecular simulations. GROMACS includes many tricks to improve speed. Its main strength, however, lies in its flexibility, and in the fact that it is in the public domain and distributed under the GNU General Public License.
    • Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J. GROMACS: fast, flexible, and free. J Comput Chem 26 (2005) 1701-1718. This paper presents an overview of the GROMACS package for molecular simulations. GROMACS includes many tricks to improve speed. Its main strength, however, lies in its flexibility, and in the fact that it is in the public domain and distributed under the GNU General Public License.
    • (2005) J Comput Chem , vol.26 , pp. 1701-1718
    • Van Der Spoel, D.1    Lindahl, E.2    Hess, B.3    Groenhof, G.4    Mark, A.E.5    Berendsen, H.J.6
  • 25
    • 17844392069 scopus 로고    scopus 로고
    • A simple method for faster nonbonded force evaluations
    • This paper introduces approximations for the evaluation of inverse distances, such that square root or division operations are not required.
    • Shen M.Y., and Freed K.F. A simple method for faster nonbonded force evaluations. J Comput Chem 26 (2005) 691-698. This paper introduces approximations for the evaluation of inverse distances, such that square root or division operations are not required.
    • (2005) J Comput Chem , vol.26 , pp. 691-698
    • Shen, M.Y.1    Freed, K.F.2
  • 26
    • 24144495573 scopus 로고    scopus 로고
    • A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
    • This paper introduces a new method for the parallel evaluation of pairwise particle interactions. Its originality lies in the reduction of the amount of data transferred between processors, taking advantage of the fact that particles only interact with neighboring particles within a given cutoff.
    • Shaw D.E. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem 26 (2005) 1318-1328. This paper introduces a new method for the parallel evaluation of pairwise particle interactions. Its originality lies in the reduction of the amount of data transferred between processors, taking advantage of the fact that particles only interact with neighboring particles within a given cutoff.
    • (2005) J Comput Chem , vol.26 , pp. 1318-1328
    • Shaw, D.E.1
  • 27
    • 0024795316 scopus 로고
    • The effects of truncating long-range forces on protein dynamics
    • Loncharich R.J., and Brooks B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6 (1989) 32-45
    • (1989) Proteins , vol.6 , pp. 32-45
    • Loncharich, R.J.1    Brooks, B.R.2
  • 28
    • 0026755515 scopus 로고
    • Cutoff size does strongly influence molecular dynamics results on solvated polypeptides
    • Schreiber H., and Steinhauser O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 31 (1992) 5856-5860
    • (1992) Biochemistry , vol.31 , pp. 5856-5860
    • Schreiber, H.1    Steinhauser, O.2
  • 29
    • 0027065111 scopus 로고
    • Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method
    • Schreiber H., and Steinhauser O. Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method. J Mol Biol 228 (1992) 909-923
    • (1992) J Mol Biol , vol.228 , pp. 909-923
    • Schreiber, H.1    Steinhauser, O.2
  • 30
    • 21144484257 scopus 로고
    • Molecular dynamics studies of solvated polypeptides: why cutoff scheme does not work
    • Schreiber H., and Steinhauser O. Molecular dynamics studies of solvated polypeptides: why cutoff scheme does not work. Chem Phys 168 (1992) 75-89
    • (1992) Chem Phys , vol.168 , pp. 75-89
    • Schreiber, H.1    Steinhauser, O.2
  • 31
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • The authors revisit the problem of artifacts introduced by cutoff schemes in MD simulation. They show that, by using a proper force-shifted spherical cutoff, it is possible to correctly model peptide dynamics in solution.
    • Beck D.A., Armen R.S., and Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 44 (2005) 609-616. The authors revisit the problem of artifacts introduced by cutoff schemes in MD simulation. They show that, by using a proper force-shifted spherical cutoff, it is possible to correctly model peptide dynamics in solution.
    • (2005) Biochemistry , vol.44 , pp. 609-616
    • Beck, D.A.1    Armen, R.S.2    Daggett, V.3
  • 32
    • 0033850287 scopus 로고    scopus 로고
    • On the truncation of long-range electrostatic interactions in DNA
    • Norberg J., and Nilsson L. On the truncation of long-range electrostatic interactions in DNA. Biophys J 79 (2000) 1537-1553
    • (2000) Biophys J , vol.79 , pp. 1537-1553
    • Norberg, J.1    Nilsson, L.2
  • 33
    • 0032757340 scopus 로고    scopus 로고
    • Study of the electrostatics treatment in molecular dynamics simulations
    • Garemyr R., and Elofsson A. Study of the electrostatics treatment in molecular dynamics simulations. Proteins 37 (1999) 417-428
    • (1999) Proteins , vol.37 , pp. 417-428
    • Garemyr, R.1    Elofsson, A.2
  • 34
    • 2942572789 scopus 로고    scopus 로고
    • Complexity and convergence of electrostatic and van der Waals energies within PME and cutoff methods
    • Varekova R.D., Koca J., and Zhan C.G. Complexity and convergence of electrostatic and van der Waals energies within PME and cutoff methods. Int J Mol Sci 5 (2004) 154-173
    • (2004) Int J Mol Sci , vol.5 , pp. 154-173
    • Varekova, R.D.1    Koca, J.2    Zhan, C.G.3
  • 37
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an n log n method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: an n log n method for Ewald sums in large systems. J Chem Phys 99 (1993) 10089-10092
    • (1993) J Chem Phys , vol.99 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 38
    • 0035870662 scopus 로고    scopus 로고
    • Multigrid methods for classical molecular dynamics simulations of biomolecules
    • Sagui C., and Darden T. Multigrid methods for classical molecular dynamics simulations of biomolecules. J Chem Phys 114 (2001) 6578-6591
    • (2001) J Chem Phys , vol.114 , pp. 6578-6591
    • Sagui, C.1    Darden, T.2
  • 39
    • 0037197257 scopus 로고    scopus 로고
    • Multiple grid methods for classical molecular dynamics
    • Skeel R.D., Tezcan I., and Hardy D.J. Multiple grid methods for classical molecular dynamics. J Comput Chem 23 (2002) 673-684
    • (2002) J Comput Chem , vol.23 , pp. 673-684
    • Skeel, R.D.1    Tezcan, I.2    Hardy, D.J.3
  • 40
    • 22944460220 scopus 로고    scopus 로고
    • Gaussian split Ewald: a fast Ewald mesh method for molecular simulation
    • The authors propose a new Ewald mesh method for computing the electrostatic interactions between particles in the case of explicit solvent with PBCs. This method involves two stages of charge spreading on the mesh; it can be used with both a real-space and a Fourier-space solver of the Poisson equation. Noteworthy in this paper is the introduction of a uniform framework that describes the differences between existing Ewald mesh methods.
    • Shan Y., Klepeis J.L., Eastwood M.P., Dror R.O., and Shaw D.E. Gaussian split Ewald: a fast Ewald mesh method for molecular simulation. J Chem Phys 122 (2005) 54101. The authors propose a new Ewald mesh method for computing the electrostatic interactions between particles in the case of explicit solvent with PBCs. This method involves two stages of charge spreading on the mesh; it can be used with both a real-space and a Fourier-space solver of the Poisson equation. Noteworthy in this paper is the introduction of a uniform framework that describes the differences between existing Ewald mesh methods.
    • (2005) J Chem Phys , vol.122 , pp. 54101
    • Shan, Y.1    Klepeis, J.L.2    Eastwood, M.P.3    Dror, R.O.4    Shaw, D.E.5
  • 42
    • 20444473641 scopus 로고    scopus 로고
    • MDSIMAID: automatic parameter optimization in fast electrostatic algorithms
    • MDSimAID is a recommender system that optimizes parallel fast electrostatics solvers and presents recommended parameters to the user. It is part of a general effort (see [43]) to facilitate the use and development of new methods for computing electrostatic interactions in explicit solvent models.
    • Crocker M.S., Hampton S.S., Matthey T., and Izaguirre J.A. MDSIMAID: automatic parameter optimization in fast electrostatic algorithms. J Comput Chem 26 (2005) 1021-1031. MDSimAID is a recommender system that optimizes parallel fast electrostatics solvers and presents recommended parameters to the user. It is part of a general effort (see [43]) to facilitate the use and development of new methods for computing electrostatic interactions in explicit solvent models.
    • (2005) J Comput Chem , vol.26 , pp. 1021-1031
    • Crocker, M.S.1    Hampton, S.S.2    Matthey, T.3    Izaguirre, J.A.4
  • 44
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi I.G., Sperb R., Smith P.E., and van Gunsteren W.F. A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102 (1995) 5451-5459
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    van Gunsteren, W.F.4
  • 45
    • 23744467771 scopus 로고    scopus 로고
    • Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations
    • The authors describe a new scheme for computing electrostatic interactions in explicit solvent with PBCs that combines a mesh or lattice-sum approach and a reaction-field approach. They show that there is continuity between the lattice-sum and reaction-field schemes, and unify them into a common framework.
    • Heinz T.N., and Hunenberger P.H. Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations. J Chem Phys 123 (2005) 34107. The authors describe a new scheme for computing electrostatic interactions in explicit solvent with PBCs that combines a mesh or lattice-sum approach and a reaction-field approach. They show that there is continuity between the lattice-sum and reaction-field schemes, and unify them into a common framework.
    • (2005) J Chem Phys , vol.123 , pp. 34107
    • Heinz, T.N.1    Hunenberger, P.H.2
  • 46
    • 22944443583 scopus 로고    scopus 로고
    • Isotropic periodic sum: a method for the calculation of long-range interactions
    • This paper describes a new approach to the calculation of long-range interactions in explicit solvent models. It defines a local region around each particle and describes the remaining region as images of the local region, distributed statistically in an isotropic and periodic way.
    • Wu X., and Brooks B.R. Isotropic periodic sum: a method for the calculation of long-range interactions. J Chem Phys 122 (2005) 44107. This paper describes a new approach to the calculation of long-range interactions in explicit solvent models. It defines a local region around each particle and describes the remaining region as images of the local region, distributed statistically in an isotropic and periodic way.
    • (2005) J Chem Phys , vol.122 , pp. 44107
    • Wu, X.1    Brooks, B.R.2
  • 47
    • 19644381543 scopus 로고    scopus 로고
    • Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation
    • The authors describe a new, rapid method for the calculation of electrostatic interactions between particles. It does not require a cutoff distance and the computing time scales linearly with the number of particles or charges. The main idea presented is to replace the double sum in the Coulomb summation with the product of two simple sums, using tricks introduced to compute Euler sums. It does require the inverse of the distance to be approximated with a polynomial.
    • Petrella R.J., and Karplus M. Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation. J Comput Chem 26 (2005) 755-787. The authors describe a new, rapid method for the calculation of electrostatic interactions between particles. It does not require a cutoff distance and the computing time scales linearly with the number of particles or charges. The main idea presented is to replace the double sum in the Coulomb summation with the product of two simple sums, using tricks introduced to compute Euler sums. It does require the inverse of the distance to be approximated with a polynomial.
    • (2005) J Comput Chem , vol.26 , pp. 755-787
    • Petrella, R.J.1    Karplus, M.2
  • 49
    • 0037627173 scopus 로고    scopus 로고
    • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study
    • Hunenberger P.H., and McCammon J.A. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem 78 (1999) 69-88
    • (1999) Biophys Chem , vol.78 , pp. 69-88
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 50
    • 0038683517 scopus 로고    scopus 로고
    • Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study
    • Hunenberger P.H., and McCammon J.A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study. J Chem Phys 110 (1999) 1856-1872
    • (1999) J Chem Phys , vol.110 , pp. 1856-1872
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 51
    • 0343005873 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation
    • Weber W., Hunenberger P.H., and McCammon J.A. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B104 (2000) 3668-3675
    • (2000) J Phys Chem , vol.B104 , pp. 3668-3675
    • Weber, W.1    Hunenberger, P.H.2    McCammon, J.A.3
  • 52
    • 25144520249 scopus 로고    scopus 로고
    • On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini
    • The authors re-examine the problem of artifacts detected in molecular simulations based on Ewald summation. Using simulations of octa-alanine peptides, they show that the artifacts are more a consequence of poor sampling than of the Ewald summation technique.
    • Villarreal M.A., and Montich G.G. On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini. J Biomol Struct Dyn 23 (2005) 135-142. The authors re-examine the problem of artifacts detected in molecular simulations based on Ewald summation. Using simulations of octa-alanine peptides, they show that the artifacts are more a consequence of poor sampling than of the Ewald summation technique.
    • (2005) J Biomol Struct Dyn , vol.23 , pp. 135-142
    • Villarreal, M.A.1    Montich, G.G.2
  • 53
    • 4143094922 scopus 로고    scopus 로고
    • The influence of simulation conditions in molecular dynamics investigations of model beta-sheet peptides
    • Monticelli L., and Colombo G. The influence of simulation conditions in molecular dynamics investigations of model beta-sheet peptides. Theoretical Chemical Accounts 3 (2004) 145-157
    • (2004) Theoretical Chemical Accounts , vol.3 , pp. 145-157
    • Monticelli, L.1    Colombo, G.2
  • 55
    • 18744387415 scopus 로고    scopus 로고
    • Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
    • An excellent review of potential energy functions for molecular simulations.
    • Jorgensen W.L., and Tirado-Rives J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci USA 102 (2005) 6665-6670. An excellent review of potential energy functions for molecular simulations.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6665-6670
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 56
    • 33645724429 scopus 로고
    • Structure and properties of neat liquids using non additive molecular mechanics: water, methanol, and N-methylacetamide
    • Caldwell J.W., and Kollman P.A. Structure and properties of neat liquids using non additive molecular mechanics: water, methanol, and N-methylacetamide. J Phys Chem 99 (1995) 6208-6219
    • (1995) J Phys Chem , vol.99 , pp. 6208-6219
    • Caldwell, J.W.1    Kollman, P.A.2
  • 57
    • 0032568609 scopus 로고    scopus 로고
    • Is polarization important in cation-pi interactions?
    • Cubero E., Luque F.J., and Orozco M. Is polarization important in cation-pi interactions?. Proc Natl Acad Sci USA 95 (1998) 5976-5980
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 5976-5980
    • Cubero, E.1    Luque, F.J.2    Orozco, M.3
  • 58
    • 77949975511 scopus 로고    scopus 로고
    • Potentials and algorithms for incorporating polarizability in computer simulations
    • Rick S.W., and Stuart S.J. Potentials and algorithms for incorporating polarizability in computer simulations. Rev Comp Chem 18 (2002) 89-146
    • (2002) Rev Comp Chem , vol.18 , pp. 89-146
    • Rick, S.W.1    Stuart, S.J.2
  • 59
    • 0036882094 scopus 로고    scopus 로고
    • Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests
    • Kaminski G.A., Stern H.A., Berne B.J., Friesner R.A., Cao Y.X., Murphy R.B., Zhou R., and Halgren T.A. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 23 (2002) 1515-1531
    • (2002) J Comput Chem , vol.23 , pp. 1515-1531
    • Kaminski, G.A.1    Stern, H.A.2    Berne, B.J.3    Friesner, R.A.4    Cao, Y.X.5    Murphy, R.B.6    Zhou, R.7    Halgren, T.A.8
  • 60
    • 4043057278 scopus 로고    scopus 로고
    • CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
    • Patel S., Mackerell Jr. A.D., and Brooks III C.L. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 25 (2004) 1504-1514
    • (2004) J Comput Chem , vol.25 , pp. 1504-1514
    • Patel, S.1    Mackerell Jr., A.D.2    Brooks III, C.L.3
  • 61
    • 7544244858 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields
    • Baucom J., Transue T., Fuentes-Cabrera M., Krahn J.M., Darden T.A., and Sagui C. Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields. J Chem Phys 121 (2004) 6998-7008
    • (2004) J Chem Phys , vol.121 , pp. 6998-7008
    • Baucom, J.1    Transue, T.2    Fuentes-Cabrera, M.3    Krahn, J.M.4    Darden, T.A.5    Sagui, C.6
  • 62
    • 18744402303 scopus 로고    scopus 로고
    • Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator
    • The authors have developed a polarizable empirical force-field based on the classical Drude oscillator model. They incorporated it into CHARMM and have tested it in a 1000 ps simulation of a DNA octamer in a box of water with sodium counterions, again proving the feasibility of using polarizable force-fields (see also [59-61]).
    • Anisimov V.M., Lamoureux G., Vorobyov I.G., Huang N., Roux B., and Mackerell Jr. A.D. Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. J Chem Theory Comput 1 (2005) 153-168. The authors have developed a polarizable empirical force-field based on the classical Drude oscillator model. They incorporated it into CHARMM and have tested it in a 1000 ps simulation of a DNA octamer in a box of water with sodium counterions, again proving the feasibility of using polarizable force-fields (see also [59-61]).
    • (2005) J Chem Theory Comput , vol.1 , pp. 153-168
    • Anisimov, V.M.1    Lamoureux, G.2    Vorobyov, I.G.3    Huang, N.4    Roux, B.5    Mackerell Jr., A.D.6
  • 63
    • 0037963208 scopus 로고    scopus 로고
    • An empirical model for the electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants
    • Wisz M.S., and Hellinga H.W. An empirical model for the electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins 51 (2003) 360-377
    • (2003) Proteins , vol.51 , pp. 360-377
    • Wisz, M.S.1    Hellinga, H.W.2
  • 64
    • 24144489511 scopus 로고    scopus 로고
    • Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins
    • The authors have developed a pragmatic approach to implicit solvation that approximates solvent screening by individually scaling the partial charges of the atoms, so as to reproduce electrostatic interactions obtained from a PB analysis. The scaled charges are consequently maintained as fixed during molecular simulations.
    • Schwarzl S.M., Huang D., Smith J.C., and Fisher S. Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins. J Comput Chem 26 (2005) 1359-1371. The authors have developed a pragmatic approach to implicit solvation that approximates solvent screening by individually scaling the partial charges of the atoms, so as to reproduce electrostatic interactions obtained from a PB analysis. The scaled charges are consequently maintained as fixed during molecular simulations.
    • (2005) J Comput Chem , vol.26 , pp. 1359-1371
    • Schwarzl, S.M.1    Huang, D.2    Smith, J.C.3    Fisher, S.4
  • 65
    • 0346971105 scopus 로고    scopus 로고
    • 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., and Brooks III C.L. Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 25 (2004) 265-284
    • (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
  • 66
    • 0042139644 scopus 로고    scopus 로고
    • Comparison of generalized Born and Poisson models: energetics and dynamics of HIV protease
    • David L., Luo R., and Gilson M. Comparison of generalized Born and Poisson models: energetics and dynamics of HIV protease. J Comput Chem 21 (2000) 295-309
    • (2000) J Comput Chem , vol.21 , pp. 295-309
    • David, L.1    Luo, R.2    Gilson, M.3
  • 67
    • 0037103014 scopus 로고    scopus 로고
    • Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation
    • Lu B.Z., Chen W.Z., Wang C.X., and Xu X.J. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins 48 (2002) 497-504
    • (2002) Proteins , vol.48 , pp. 497-504
    • Lu, B.Z.1    Chen, W.Z.2    Wang, C.X.3    Xu, X.J.4
  • 68
    • 0036771626 scopus 로고    scopus 로고
    • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    • Luo R., David L., and Gilson M.K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem 23 (2002) 1244-1253
    • (2002) J Comput Chem , vol.23 , pp. 1244-1253
    • Luo, R.1    David, L.2    Gilson, M.K.3
  • 69
    • 0038650794 scopus 로고    scopus 로고
    • Protocol for MM/PBSA molecular dynamics simulations of proteins
    • Fogolari F., Brigo A., and Molinari H. Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J 85 (2003) 159-166
    • (2003) Biophys J , vol.85 , pp. 159-166
    • Fogolari, F.1    Brigo, A.2    Molinari, H.3
  • 70
    • 9244259076 scopus 로고    scopus 로고
    • Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
    • Prabhu N.V., Zhu P., and Sharp K.A. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J Comput Chem 25 (2004) 2049-2064
    • (2004) J Comput Chem , vol.25 , pp. 2049-2064
    • Prabhu, N.V.1    Zhu, P.2    Sharp, K.A.3
  • 71
    • 17744382377 scopus 로고    scopus 로고
    • One and two-body decomposable Poisson-Boltzmann methods for protein design calculations
    • One-body and two-body decomposable PB methods are proposed for computing electrostatic interactions. These approximate methods were specifically developed for protein design.
    • Marshall S.A., Vizcarra C.L., and Mayo S.L. One and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci 14 (2005) 1293-1304. One-body and two-body decomposable PB methods are proposed for computing electrostatic interactions. These approximate methods were specifically developed for protein design.
    • (2005) Protein Sci , vol.14 , pp. 1293-1304
    • Marshall, S.A.1    Vizcarra, C.L.2    Mayo, S.L.3
  • 72
    • 21244431972 scopus 로고    scopus 로고
    • Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method
    • The authors propose a new approach for calculating electrostatics forces among solvated molecules when the electric field is obtained by solving the linearized PB equation. They use the variational principle in the context of BEM. This approach does not require the calculation of the stress tensor on the surface of the molecule and therefore avoids the problem of hypersingularity.
    • Lu B., Zhang D., and McCammon J.A. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys 122 (2005) 214102. The authors propose a new approach for calculating electrostatics forces among solvated molecules when the electric field is obtained by solving the linearized PB equation. They use the variational principle in the context of BEM. This approach does not require the calculation of the stress tensor on the surface of the molecule and therefore avoids the problem of hypersingularity.
    • (2005) J Chem Phys , vol.122 , pp. 214102
    • Lu, B.1    Zhang, D.2    McCammon, J.A.3
  • 73
    • 33845910351 scopus 로고    scopus 로고
    • Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals
    • ••] are still at the developmental stage.
    • ••] are still at the developmental stage.
    • (2005) J Chem Phys , vol.123 , pp. 084904
    • Lu, B.1    Cheng, X.2    Hou, T.3    McCammon, J.A.4
  • 74
    • 22844436061 scopus 로고    scopus 로고
    • Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2
    • A new way of solving the PB equation on a special-purpose hardware chip is presented. The author reports acceleration factors of up to 40-fold with no loss of accuracy compared with conventional approaches.
    • Hofinger S. Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2. J Comput Chem 26 (2005) 1148-1154. A new way of solving the PB equation on a special-purpose hardware chip is presented. The author reports acceleration factors of up to 40-fold with no loss of accuracy compared with conventional approaches.
    • (2005) J Comput Chem , vol.26 , pp. 1148-1154
    • Hofinger, S.1
  • 75
    • 0344778061 scopus 로고
    • Semi-analytical treatment of solvation for molecular mechanics and dynamics
    • Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semi-analytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112 (1990) 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
  • 76
    • 14544285906 scopus 로고    scopus 로고
    • Comparative study of generalized Born models: Born radii and peptide folding
    • Four GB models are compared in terms of their ability to reproduce the results of PB calculations and their performance in the ab initio folding of two peptides. Surprisingly, the method that is most successful in reproducing PB results is not the most effective in the folding experiments.
    • Zhu J., Alexov E., and Honig B. Comparative study of generalized Born models: Born radii and peptide folding. J Phys Chem B 109 (2005) 3008-3022. Four GB models are compared in terms of their ability to reproduce the results of PB calculations and their performance in the ab initio folding of two peptides. Surprisingly, the method that is most successful in reproducing PB results is not the most effective in the folding experiments.
    • (2005) J Phys Chem B , vol.109 , pp. 3008-3022
    • Zhu, J.1    Alexov, E.2    Honig, B.3
  • 77
    • 18744382161 scopus 로고    scopus 로고
    • Comparative study of generalized Born models: protein dynamics
    • ••] are compared in terms of their performance in retaining native properties of protein structures during MD simulations. The highlight of this paper is the development of a statistical framework to verify that the results of MD simulations are meaningful.
    • ••] are compared in terms of their performance in retaining native properties of protein structures during MD simulations. The highlight of this paper is the development of a statistical framework to verify that the results of MD simulations are meaningful.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6760-6764
    • Fan, H.1    Mark, A.E.2    Zhu, J.3    Honig, B.4
  • 78
    • 23144457576 scopus 로고    scopus 로고
    • H++: a server for estimating pKas and adding missing hydrogens to macromolecules
    • as and related characteristics of biomolecules. This server is designed to facilitate access to electrostatics analysis by a large community, including non-experts.
    • as and related characteristics of biomolecules. This server is designed to facilitate access to electrostatics analysis by a large community, including non-experts.
    • (2005) Nucleic Acids Res , vol.33
    • Gordon, J.C.1    Myers, J.B.2    Folta, T.3    Shoja, V.4    Heath, L.S.5    Onufriev, A.6
  • 80
    • 2442693239 scopus 로고    scopus 로고
    • Macroscopic electrostatic models for protonation states in proteins
    • Bashford D. Macroscopic electrostatic models for protonation states in proteins. Front Biosci 9 (2004) 1082-1099
    • (2004) Front Biosci , vol.9 , pp. 1082-1099
    • Bashford, D.1
  • 81
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32 (2004) W665-W667
    • (2004) Nucleic Acids Res , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 82
    • 33645961828 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: method and error assessment
    • Gilson M.K., Sharp K., and Honig B. Calculating the electrostatic potential of molecules in solution: method and error assessment. Proteins 4 (1988) 7-18
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Sharp, K.2    Honig, B.3
  • 83
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: application to microtubules and the ribosome
    • Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98 (2001) 10037-10041
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 84
    • 0035971738 scopus 로고    scopus 로고
    • A smooth permittivity function for Poisson Boltzmann solvation methods
    • Grant J.A., Pickup B.T., and Nicholls A. A smooth permittivity function for Poisson Boltzmann solvation methods. J Comput Chem 22 (2001) 608-640
    • (2001) J Comput Chem , vol.22 , pp. 608-640
    • Grant, J.A.1    Pickup, B.T.2    Nicholls, A.3
  • 85
    • 2542429164 scopus 로고    scopus 로고
    • Efficient solution technique for solving the Poisson-Boltzmann equations
    • Sayyed-Ahmad A., Tuncay K., and Ortoleva P. Efficient solution technique for solving the Poisson-Boltzmann equations. J Comput Chem 25 (2004) 1068-1074
    • (2004) J Comput Chem , vol.25 , pp. 1068-1074
    • Sayyed-Ahmad, A.1    Tuncay, K.2    Ortoleva, P.3
  • 86
    • 0026319199 scopus 로고
    • Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K., and Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11 (1991) 281-296
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.2    Honig, B.3
  • 87
    • 0346122798 scopus 로고    scopus 로고
    • GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences
    • Petrey D., and Honig B. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol 374 (2003) 492-509
    • (2003) Methods Enzymol , vol.374 , pp. 492-509
    • Petrey, D.1    Honig, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.