Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules

Journal of Computational Chemistry

Volumn 19, Issue 3, 1998, Pages 319-333

  Fraczkiewicz, Robert ^a   Braun, Werner ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Atomic solvation parameters; Avian pancreatic polypeptide; FANTOM; Monte Carlo simulation; Solvation energy; Solvent accessible surface area

Indexed keywords

EID: 0001528720     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W     Document Type: Article

References (61)

1. (a) B. Lee and F. M. Richards, J. Mol. Biol., 55, 379 (1971)
2. (b) F. M. Richards, Annu. Rev. Biophys. Bioeng., 6, 151 (1977).
3. B. Honig and A. Nichols, Science, 268, 1144 (1995).
4. P. E. Smith and B. M. Pettitt, J. Phys. Chem., 98, 9700 (1994).
5. D. Eisenberg and A. D. McLachlan, Nature, 316, 199 (1986).
6. T. Ooi, M. Oobatake, G. Némethy, and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 3086 (1987).
7. L. Chiche, L. M. Gregoret, F. E. Cohen, and P. A. Kollman, Proc. Natl. Acad. Sci. USA, 87, 3240 (1990).
8. V. P. Collura, P. J. Greaney, and B. Robson Prot. Eng., 7, 221 (1994).
9. Y. Wang, H. Zhang, and R. Scott, Prot. Sci., 4, 1402 (1995).
10. M. L. Connolly. J. Appl. Cryst., 16, 548 (1983).
11. T. J. Richmond. J. Mol. Biol., 178, 63 (1984).
12. E. Silla, F. Villar, O. Nilsson, J. L. Pascual-Ahuir, and O. Tapia, J. Mol. Graph., 8, 168 (1990).
13. B. von Freyberg and W. Braun, J. Comput. Chem., 14, 510 (1993).
14. F. Eisenhaber and P, Argos, J, Comput. Chem., 14, 1272 (1943).
15. M. L. Connolly, J. Mol. Graph., 11, 139 (1993).
16. M. Petitjean, J. Comput. Chem., 15, 507 (1994).
17. F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, J. Comput. Chem., 16, 273 (1995).
18. M. Cossi, B. Mennucci, and R. Cammi, J. Comput. Chem., 17, 57 (1996).
19. W. Braun, In Computer Simulation of Biomolecular Systems, Vol. 3, W. van Gunsteren, P. Weiner, and T. Wilkinson, Eds., ESCOM, Leiden, 1996.
20. S. J. Wodak and J. Janin, Proc. Natl. Acad. Sci. USA, 77, 1736 (1980).
21. W. Hasel, T. F. Hendrickson, and W. C. Still, Tetrahed. Comput. Methodol., 1, 103 (1988).
22. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc.,112, 6127 (1990).
23. G. 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).
24. (a) S. Sridharan, A. Nicholls, and K. A. Sharp, J. Comput. Chem., 16, 1038 (1995)
25. (b) S. Sridharan, A. Nicholls, and B. Honig, Biophys. J., 61, A174 (1992).
26. E. Meirovitch and H. Meirovirch, Biopolymers, 38, 69 (1996).
27. O. Collet and S. Premilat, Int. J. Peptide Prot. Res., 47, 239 (1996).
28. R. L. Williams J. Vila, G. Perrot, and H. A. Scheraga, Prot. Struct. Funct. Genet., 14, 110 (1992).
29. B. von Freyberg, T. J. Richmond, and W. Braun, J. Mol. Biol., 233, 275 (1993).
30. Ch. Mumenthaler and W. Braun, J. Mol. Model., 1, 1 (1995).
31. L. Wesson and D. Eisenberg, Prot. Sci., 1, 227 (1992).
32. C. A. Schiffer, J. W. Caldwell, P. A. Kollman, and R. M. Stroud, Mol. Sim., 10, 121 (1993).
33. F. Fraternali and W. F. van Gunsteren, J. Mol. biol., 256, 939 (1996).
34. M. D. Cummings, T. N. Hart, and R. J. Read, Prot. Sci., 4, 2087 (1995).
35. M. P. doCarmo, Differential Geometry of Curves and Surfaces, Prentice-Hall, Englewood Cliffs, NJ, 1976.
36. T. Schaumann, W. Braun, and K. Wüthrich, Biopolymers, 29, 679 (1990).
37. Information on how to obtain the new version of FANTOM can be found on the web page http://www. scsb.utmb.edu/fantom/fm_home.html or by e-mail request to werner@nmr.utmb.edu.
38. Vectors are printed in bold. "○" and "×" denote scalar and cross-products of two vectors, respectively. "|·|" is a vector norm.
39. 3). I has the meaning of a 3 × 3 identity matrix. K denotes set of accessible arcs belonging to the kth COI; L is the set of all accessible arcs.
40. W. Braun and N. Go, J. Mol. Biol., 186, 611 (1985).
41. G. S. Grest, B. Dünweg, and K. Kremer, Comp. Phys. Commun., 55, 269 (1989).
42. F. P. Preparata and M. I. Shamos, Computational Geometry: An Introduction, Springer-Verlag, New York, 1985.
43. J. O'Rourke, Computational Geometry in C, Cambridge University Press, New York, 1993.
44. C. Chothia, Nature, 248, 338 (1974).
45. T. L. Blundell, J. E. Pitts, I. J. Tickle, S. P. Wood, and C. W. Wu, Proc. Natl. Acad. Sci. USA, 78, 4175 (1981).
46. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer Jr., M. D. Brice, J. R. Rogers, O. Kennard, T. Schimanouchi, and M. Tasumi, J. Mol. Biol., 112, 535 (1977).
47. (a) P. Güntert, W. Braun, and K. Wüthrich, J. Mol. Biol., 217, 517 (1991)
48. (b) G. Hänggi and W. Braun, FEBS Lett., 344, 147 (1994).
49. Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 6611 (1987).
50. B. von Freyberg and W. Braun, J. Comput. Chem., 12, 1065 (1991).
51. A. Shrake and J. A. Rupley, J. Mol. Biol., 79, 351 (1973).
52. J. Vila, R. L. Williams, M. Vásquez, and H. A. Scheraga, Prot. Struct. Funct. Genet., 10, 199 (1991).
53. (a) P. J. Chang, M. E. Noelken, and J. R. Kimmel, Biochemistry, 19, 1844 (1980)
54. (b) M. E. Noelken, P. J. Chang, and J. R. Kimmel, Biochemistry. 19, 1838 (1980)
55. (c) I. Glover, I. Haneef, J. E. Pitts, S. P. Wood, D. Moss, I. J. Tickle, and T. L. Blundell, Biopolymers, 22, 293 (1983).
56. (a) F. A. Momany, R. F. McGuire, A. W. Burgess, and H. A. Scheraga, J. Phys. Chem., 79, 2361 (1975)
57. (b) G. Némethy, M. S. Pottle, and H. A. Scheraga, J. Phys. Chem., 87, 1883 (1983).
58. B. Park and M. Levitt, J. Mol. Biol., 258, 367 (1996).
59. A. Liwo, M. R. Pincus, R. J. Wawak, S. Rackovsky, and H. A. Scheraga, Proc. Sci., 2, 1715 (1993).
60. H. Zhang, C. F. Wong, T. Thacher, and H. Rabitz, Prot. Struct. Funct. Genet., 23, 218 (1995).
61. R. Koradi, M. Billeter, and K. Wüthrich, J. Mol. Graph., 14, 51 (1996).