Fast methods for simulation of biomolecule electrostatics

IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers

Volumn , Issue , 2002, Pages 466-470

  Kuo, Shihhsien S ^a   Altman, Michael D ^b   Bardhan, Jaydeep P ^a   Tidor, Bruce ^a,b   White, Jacob K ^a  

^a USA   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULE ELECTROSTATICS; COVALENT BONDING;

ELECTROSTATICS; INTEGRAL EQUATIONS; INTERCONNECTION NETWORKS; IONIC STRENGTH; MOLECULAR DYNAMICS; PARTIAL DIFFERENTIAL EQUATIONS; PROBLEM SOLVING;

COMPUTER SIMULATION;

EID: 0036907127     PISSN: 10923152     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/774572.774640     Document Type: Conference Paper

References (46)

1. M. K. Gilson, A. Rashin, R. Fine, and B. Honig. On the calculation of electroastatic interactions in proteins. Journal of Molecular Biology, 183: 503-516, 1985.
2. K. A. Sharp and B. Honig. Electrostatic interactions in macromolecules: Theory and applications. Annual Review of Biophysics and Biophysical Chemistry, 19:301-332, 1990.
3. M. E. Davis and J. A. McCammon. Electrostatics in biomolecular structure and dynamics. Chem. Rev., 90:509-521, 1990.
4. J. A. Grant, B. T. Pickup, and A. Nicholls. A smooth permittivity function for Poisson-Boltzmann solvation methods. Journal of Computational Chemistry, 22:608-640, 2001.
5. L. P. Lee and B. Tidor. Barstar is electrostatically optimized for tight-binding to barnase. Nature Structural Biology, 8:73-76, 2001.
6. L. Lee and B. Tidor. Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex. Protein Science, 10:362-377, 2000.
7. E. Kangas and B. Tidor. Electrostatic specificity in molecular ligand design. Journal of Chemical Physics, 112:9120-9131, 2000.
8. E. Kangas and B. Tidor. Electrostatic complementarity at ligand binding sites: Application to chorismate mutase. Journal of Physical Chemistry, 105:880-888, 2001.
9. Z. S. Hendsch, M. J. Nohaile, R. T. Sauer, and B. Tidor. Preferential heterodimer formation via undercompensated electrostatic interactions. Journal of the American Chemical Society, 123:1264-1265, 2001.
10. V. Lounnas, B. M. Pettitt, L. Findsen, and S. Subramaniam. A microscopic view of protein solvation. Journal of Physical Chemistry, 18:7157-7159, 1992.
11. J. A. McCammon and S. C. Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, 1987.
12. C. L. Brooks, III, M. Karplus, and B. M. Pettitt. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys., 71:1-249, 1988.
13. A. Jean-Charles, A. Nicholls, K. Sharp, B. Honig A. Tempczyk, T. F. Hendrickson, and W. C. Still. Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations. J. Am. Chem. Soc., 113:1454-1455, 1991.
14. S. W. Rick and B. J. Berne. The aqueous solvation of water: A comparison of continuum methods with molecular dynamics. J. Am. Chem. Soc., 116:3949-3954, 1994.
15. C. Tanford and J. G. Kirkwood. Theory of protein titration curves I. general equations for impenetrable spheres. Journal of the American Chemical Society, 59:5333-5339, 1957.
16. B. Honig and A. Nicholls, Classical electrostatics in biology and chemistry. Science (Washington, D.C.), 268:1144-1149, 1995.
17. J. Warwicker and H. C. Watson. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. Journal of Molecular Biology, 157:671-679, 1982.
18. J. D. Madura, J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. Ridgway-Scott, and J. A. McCammon. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics program. Computer Physics Communications, 91:57-95, 1995.
19. I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and animo-acid modification. Proteins: Structure, Function, Genetics, 1:47-59, 1986.
20. M. K. Gilson, K. A. Sharp, and B. H. Honig. Calculating the electrostatic potential of molecules in solution: Method and error assessment. Journal of Computational Chemistry, 9:327-335, 1987.
21. A. Nicholls and B. Honig. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. Journal of Computational Chemistry, 12:435-445, 1991.
22. W. Rocchia, E. Alexov, and B. Honig, Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. Journal of Physical Chemistry B, 105:6507-6514, 2001.
23. W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. Journal of Computational Chemistry, 23:128-137, 2002.
24. V. Rokhlin, Rapid solution of integral equation of classical potential theory. Journal of Computational Physics, 60:187-207, 1985.
25. L. Greengard and V. Rokhlin. A fast algorithm for particle simulations. Journal of Chemical Physics, 73:325-348, 1987.
26. K. Nabors and J. White. FASTCAP: A multipole accelerated 3-D capacitance extraction program. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 10:1447-1459, 1991.
27. B. J. Yoon and A. M. Lenhoff. A boundary element method for molecular electrostatics with electrolyte effects. Journal of Computational Chemistry, 11:1080-1086, 1990.
28. J. R. Phillips and J. K. White. A precorrected-FFT method for electrostatic analysis of complicated 3-D structures. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 16:1059-1072, 1997.
29. F. M. Richards, Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6:151-176, 1977.
30. M. L. Connolly. Analytical molecular surface calculation. Journal of Applied Crystallography, 16:548-558, 1983.
31. R. W. Hockney and J. W. Eastwood. Computer simulation using particles. Adam Hilger, 1988.
32. N. K. Rogers and M. J. Sternberg. Journal of Molecular Biology, 174:527, 1984.
33. Z. Zhou, P. Payne, M. Vasquez, N. Kuhn, and M. Levitt. Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy. J. Comput. Chem., 11:1344-1351, 1996.
34. R. J. Zauhar and R. S. Morgan. The rigorous computation of the molecular electric potential. Journal of Computational Chemistry, 9:171-187, 1988.
35. A. H. Juffer, E. F. F. Botta, B. A. M. Van Keulen, A. V. D. Ploeg, and H. J. C. Berendsen. The electric potential of a macromolecule in a solvent: A fundamental approach. Journal of Computational Physics, 97:144-171, 1991.
36. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls. The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems. Journal of Computational Chemistry, 16:898-913, 1995.
37. R. J. Zauhar and A. Varnek. A fast and space-efficient boundary element method for computing electrostatic and hydration effects in large molecules. Journal of Computational Chemistry, 17:864-877, 1996.
38. M. O. Fenley, W. K. Olson, K. Chua, and A. H. Boschitsch. Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA. Journal of Computational Chemistry, 17:976-991, 1996.
39. I. Stakgold. Boundary Value Problems of Mathematical Physics. MacMillan, 1967.
40. R. F. Harrington. Field Computation by Moment Methods. MacMillan, 1968.
41. Y. Saad and M. Schultz. GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems. SIAM Journal of Scientific and Statistical Computing, 7:856-869, 1986.
42. L. Greengard. The Rapid Evaluation of Potential Fields in Particle Systems. MIT Press, 1988.
43. J. G. Kirkwood. Theory of solutions of molecules containing widely separated charges with special application to zwitterions. Journal of Chemical Physics, 2:351, 1934.
44. Matlab v.6. Mathworks, Inc.
45. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79:926-935, 1983.
46. M. Sanner, A. J. Olson, and J. C. Spehner. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers, 38:305-320, 1996.