Treatment of geometric singularities in implicit solvent models

Journal of Chemical Physics

Volumn 126, Issue 24, 2007, Pages

  Yu, Sining ^a   Geng, Weihua ^a   Wei, G W ^a,b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CUSPS; GEOMETRIC SINGULARITIES; IMPLICIT SOLVENT MODELS; MATCHED INTERFACE AND BOUNDARY (MIB);

BOLTZMANN EQUATION; COMPUTATIONAL GEOMETRY; ELECTROSTATICS; INTERFACES (MATERIALS); POISSON EQUATION; PROTEINS;

SOLVENTS;

CARBON; PROTEIN; SOLVENT;

ALGORITHM; ARTICLE; BIOPHYSICS; CHEMISTRY; CONFORMATION; ELECTRICITY; ELECTROCHEMISTRY; METHODOLOGY; MONTE CARLO METHOD; PHYSICAL CHEMISTRY; REPRODUCIBILITY; STATISTICAL MODEL; SURFACE PROPERTY; THEORETICAL MODEL; THERMODYNAMICS;

ALGORITHMS; BIOPHYSICS; CARBON; CHEMISTRY, PHYSICAL; ELECTROCHEMISTRY; ELECTROSTATICS; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; MONTE CARLO METHOD; PROTEINS; REPRODUCIBILITY OF RESULTS; SOLVENTS; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 34547352376     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2743020     Document Type: Article

References (62)

1. P. Koehl, Curr. Opin. Struct. Biol. 16, 142 (2006).
2. C. L. Vizcarra and S. L. Mayo, Curr. Opin. Struct. Biol. 9, 622 (2005).
3. N. A. Baker, Curr. Opin. Struct. Biol. 15, 137 (2005).
4. M. Feig and C. L. Brooks III, Curr. Opin. Struct. Biol. 14, 217 (2004).
5. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1591 (1997).
6. K. E. Forsten, R. E. Kozack, D. A. Lauffenburger, and S. Subramaniam, J. Phys. Chem. 98, 5580 (1994).
7. B. Honig and A. Nicholls, Science 268, 1144 (1995).
8. B. Roux and T. Simonson, Biophys. Chem. 78, 1 (1999).
9. K. A. Sharp and B. Honig, Annu. Rev. Biophys. Biophys. Chem. 19, 301 (1990).
10. Y. N. Vorobjev and H. A. Scheraga, J. Comput. Chem. 18, 569 (1997).
11. R. J. Zauhar and R. S. Morgan, J. Mol. Biol. 186, 815 (1985).
12. J. Warwicker and H. C. Watson, J. Mol. Biol. 154, 671 (1982).
13. F. Fogolari, A. Brigo, and H. Molinari, Biophys. J. 85, 159 (2003).
14. P. A. Kollman I. Massova, C. Reyes, Acc. Chem. Res. 33, 889 (2000).
15. J. M. J. Swanson, R. H. Henchman, and J. A. McCammon, Biophys. J. 86, 67 (2004).
16. R. E. Georgescu, E. G. Alexov, and M. R. Gunner, Biophys. J. 83, 1731 (2002).
17. J. E. Nielsen and J. A. McCammon, Protein Sci. 12, 313 (2003).
18. J. Warwicker, Protein Sci. 13, 2793 (2004).
19. Q. Lu and R. Luo, J. Chem. Phys. 119, 11035 (2003).
20. N. V. Prabhu, P. Zhu, and K. A. Sharp, J. Comput. Chem. 25, 2049 (2004).
21. M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks III, J. Comput. Chem. 25, 265 (2004).
22. B. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971).
23. M. L. Connolly, J. Appl. Crystallogr. 18, 499 (1985).
24. F. Eisenhaber and P. Argos, J. Comput. Chem. 14, 1272 (1993).
25. V. Gogonea and E. Osawa, Supramol. Chem. 3, 303 (1994).
26. M. F. Sanner, A. J. Olson, and J. C. Spehner, Biopolymers 38, 305 (1996).
27. J. A. Grant, B. T. Pickup, and A. Nicholls, J. Comput. Chem. 22, 608 (2001).
28. W. Im, D. Beglov, and B. Roux, Comput. Phys. Commun. 111, 59 (1998).
29. J. M. J. Swanson, J. Mongan, and J. A. McCammon, J. Phys. Chem. 109, 14769 (2005).
30. B. Z. Lu, W. Z. Chen, C. X. Wang, and X. J. Xu, Proteins 48, 497 (2002).
31. R. Luo, L. David, and M. K. Gilson, J. Comput. Chem. 23, 1244 (2002).
32. N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 98, 10037 (2001).
33. N. A. Baker, D. Sept, M. J. Holst, and J. A. McCammon, IBM J. Res. Dev. 45, 427 (2001).
34. M. Holst and F. Saied, J. Comput. Chem. 14, 105 (1993).
35. A. Bordner and G. Huber, J. Comput. Chem. 24, 353 (2003).
36. A. Boschitsch, M. Fenley, and H.-X. Zhou, J. Phys. Chem. B 106, 2741 (2002).
37. A. Boschitsch and M. Fenley, J. Comput. Chem. 25, 935 (2004).
38. A. Juffer, E. Botta, B. van Keulen, A. van der Ploeg, and H. Berendsen, J. Comput. Phys. 97, 144 (1991).
39. J. Liang and S. Subranmaniam, Biophys. J. 73, 1830 (1997).
40. I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, Proteins 1, 47 (1986).
41. W. Rocchia, E. Alexov, and B. Honig, J. Phys. Chem. B 105, 6507 (2001).
42. M. E. Davis, J. D. Madura, B. A. Luty, and J. A. McCammon, Comput. Phys. Commun. 62, 187 (1991).
43. M. Holst, N. Baker, and F. Wang, J. Comput. Chem. 21, 1319 (2000).
44. N. Baker, M. Holst, and F. Wang, J. Comput. Chem. 21, 1343 (2000).
45. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
46. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1570 (1997).
47. P. E. Dyshlovenko, Comput. Phys. Commun. 147, 335 (2002).
48. C. S. Peskin, J. Comput. Phys. 25, 220 (1977).
49. R. J. LeVeque and Z. L. Li, SIAM (Soc. Ind. Appl. Math.) J. Numer. Anal. 31, 1019 (1994).
50. R. P. Fedkiw, T. Aslam, B. Merriman, and S. Osher, J. Comput. Phys. 152, 457 (1999).
51. I. Babuška, Computing 5, 207 (1970).
52. A. Mayo, SIAM (Soc. Ind. Appl. Math.) J. Numer. Anal. 21, 285 (1984).
53. S. Zhao and G. W. Wei, J. Comput. Phys. 200, 60 (2004).
54. Y. C. Zhou, S. Zhao, M. Feig, and G. W. Wei, J. Comput. Phys. 213, 1 (2006).
55. Y. C. Zhou and G. W. Wei, J. Comput. Phys. 219, 228 (2006).
56. S. Hou and X.-D. Liu, J. Comput. Phys. 202, 411 (2005).
57. S. N. Yu, Y. C. Zhou, and G. W. Wei, J. Comput. Phys. 224, 729 (2007).
58. Y. C. Zhou, M. Feig, and G. W. Wei, J. Comput. Chem. (to be published).
59. J. G. Kirkwood, J. Chem. Phys. 7, 351 (1934).
60. S. N. Yu and G. W. Wei, J. Comput. Phys. (to be published).
61. W. H. Geng, S. N. Yu, and G. W. Wei, J. Comput. Chem. (to be published).
62. A. D. MacKerell, Jr., D. Bashford, M. Bellott, J. Phys. Chem. 102, 3586 (1998).