A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent

Journal of Computational Chemistry

Volumn 18, Issue 4, 1997, Pages 569-583

  Vorobjev, Yury N ^a   Scheraga, Harold A ^a  

^a Cornell University ^*  (United States)

Author keywords

Fast multigrid boundary element method; Macromolecular electrostatic calculations; Poisson equation

Indexed keywords

EID: 0001445346     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199703)18:4<569::AID-JCC10>3.0.CO;2-B     Document Type: Article

References (42)

1. W. Kauzmann, Adv. Protein Chem., 14, 1 (1959).
2. C. Tanford, Adv. Protein Chem., 24, 1 (1970).
3. K. A. Dill, Biochemistry, 29, 7133 (1990).
4. J. Applequist and P. Doty, In Polyamino Acids, Polypeptides and Proteins, M. A. Stahmann, Ed., Univ. of Wisconsin Press, Madison, WI, 1962, p. 161.
5. A.-S. Yang and B. Honig, J. Mol. BioL, 231, 459 (1993).
6. Y. N. Vorobjev, H. A. Scheraga, B. Hitz, and B. Honig, J. Phys. Chem., 98, 10940 (1994).
7. K. A. Sharp and B. Honig, Annu. Rev. Biophys. Biophys. Chem., 19, 301 (1990).
8. M. E. Davis and ]. A. McCammon, J. Comput. Chem., 11, 401 (1990).
9. A. A. Rashin, Prog. Biophys. Mol. BioL, 60, 73 (1993).
10. D. Sitkoff, K. A. Sharp, and B. Honig, J. Phys. Chem., 98, 1978 (1994).
11. J. Warwicker, and H. C. Watson, J. Mol. BioL, 157, 671 (1982).
12. R. J. Zauhar and R. S. Morgan, J. Comput. Chem., 9, 171 (1988).
13. A. A. Rashin, J. Phys. Chem., 94, 1725 (1990).
14. A. H. Juffer, E. F. F. Botta, A. M. Bert, B. A. M. van Keulen, A. Van der Ploeg, and H. J. C. Berendsen, J. Comp. Phys., 97, 144 (1991).
15. K. Sharp, J. Comput. Chem., 12, 454 (1991).
16. A. Nicholls and B. Honig, J. Comput. Chem., 12, 435 (1991).
17. C. Niedermeier and K. Schulten, Mol. Simul., 8, 361 (1992).
18. M. K. Gilson, J. A. McCammon, and J. D. Madura, J. Comput. Chem., 16, 1081 (1995).
19. Y. N. Vorobjev, J. A. Grant, and H. A. Scheraga, J. Am. Chem. Soc., 114, 3189 (1992).
20. W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes in C, Cambridge University Press, Cambridge, U.K., 1988.
21. A. Brandt, In Multi-Grid Methods, W. Hackbusch and U. Trottenberg, Eds., Springer-Verlag, New York, 1982, p. 220.
22. M. ]. Holst and F. Saied, J. Comput. Chem., 14, 105 (1993).
23. H. Oberoi and N. M. Allewell, Biophys. }., 65, 48 (1993).
24. M. J. Holst and F. Saied, J. Comput. Chem., 16, 337 (1995).
25. R. E. Bruccoleri, J. Comput. Chem., 14, 1417 (1993).
26. K. C. Smith and B. Honig, Proteins, 18, 119 (1994).
27. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls, J. Comput. Chem., 16, 898 (1995).
28. Y. N. Vorobjev and H. A. Scheraga, J. Phys. Chem., 97, 4855 (1993).
29. Y. N. Vorobjev, H. A. Scheraga, and B. Honig, J. Phys. Chem., 99, 7180 (1995).
30. M. L. Connolly, J. Appl. Crystallogr., 16, 548 (1983).
31. M. L. Connolly, J. Am. Chem. Soc., 107, 1118 (1985).
32. M. A. Jawson and G. T. Symm, Integral Equation Methods in Potential Theory and Elastostatics, Academic Press, New York, 1977.
33. A. A. Rashin and K. Namboodiri, J. Phys. Chem., 91, 6003 (1987).
34. J. A. Grant, R. L. Williams, and H. A. Scheraga, Biopolymers, 30, 929 (1990).
35. E. O. Purisima and S. H. Nilar, J. Comput. Chem., 16, 681 (1995).
36. L. Greengard and V. Rokhlin, J. Comp. Phys., 73, 325 (1987).
37. C. Perrot, B. Cheng, K. D. Gibson, J. Vila, K. A. Palmer, A. Nayeem, B. Maigret, and H. A. Scheraga, J. Comput. Chem., 13, 1 (1992).
38. B. J. Yoon and A. M. Lenhoff, J. Comput. Chem., 11, 1080 (1990).
39. J. Antosiewicz, J. A. McCammon, and M. K. Gilson, J. Mol. Biol, 238, 415 (1994).
40. B. Honig, Department of Biochemistry of Columbia University, personal communication (1996).
41. D. R. Ripoll, Y. N. Vorobjev, A. Liwo, J. A. Vila, and H. A. Scheraga, J. Mol. Biol., 264, 770 (1996).
42. Y. N. Vorobjev, unpublished results.