The weighted-volume derivative of a space-filling diagram

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 5, 2003, Pages 2203-2208

  Edelsbrunner, Herbert ^a,b   Koehl, Patrice ^c  

^a Duke University   (United States)

^b Raindrop Geomagic   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Delaumay triangulation; Implicit solvent models; Molecular dynamics; Spheres

Indexed keywords

ARTICLE; CALCULATION; CHEMICAL STRUCTURE; MACROMOLECULE; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR MECHANICS; PRIORITY JOURNAL;

BIOPHYSICS; MODELS, MOLECULAR; MODELS, THEORETICAL;

EID: 0037418171     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0537830100     Document Type: Article

References (44)

1. Privalov, P. L. & Gill, S. G. (1988) Adv. Protein Chem. 39, 191-234.
2. Richards, F. M. (1977) Annu. Rev. Biophys. Bioeng. 6, 151-176.
3. Morild, E. (1981) Adv. Protein Chem. 34, 93-166.
4. Tsai, J., Taylor, R., Chothia, C. & Gerstein, M. (1999) J. Mol. Biol. 290, 253-266.
5. Nadassy, K., Tomás-Oliveira, I., Alberts, I., Janin, J. & Wodak, S. J. (2001) Nucleic Acids Res. 29, 3362-3376.
6. Tsai, J. & Gerstein, M. (2002) Bioinformatics 18, 985-995.
7. Pontius, J., Richelle, J. & Wodak, S. J. (1996) J. Mol. Biol. 264, 121-136.
8. Gerstein, M., Sonnhammer, E. L. L. & Chothia, C. (1994) J. Mol. Biol. 236, 1067-1078.
9. Richards, F. M. (1974) J. Mol. Biol. 82, 1-14.
10. Rashin, A. A., Iofin, M. & Honig, B. (1986) Biochemistry 25, 3619-3625.
11. Pettitt, B. M. & Karplus, M. (1985) Chem. Phys. Lett. 121, 194-201.
12. Kang, Y. K., Nemethy, G. & Scheraga, H. A. (1987) J. Phys. Chem. 91, 4105-4109.
13. Still, W. C., Tempczyk, A., Hawley, R. C. & Hendrikson, T. (1990) J. Am. Chem. Soc. 112, 6127-6129.
14. Bashford, D. & Case, D. A. (2000) Annu. Rev. Phys. Chem. 51, 129-152.
15. Eisenberg, D. & McLachlan, A. (1986) Nature 319, 199-203.
16. Ooi, T., Oobatake, M., Nemethy, G. & Scheraga, H. (1987) Proc. Natl. Acad. Sci. USA 84, 3086-3090.
17. Simonson, T. & Brünger, A. T. (1994) J. Phys. Chem. 98, 4683-4694.
18. Lum, K., Chandler, D. & Weeks, J. D. (1999) J. Phys. Chem. B 103, 4570-4577.
19. Gibson, K. & Scheraga, H. (1967) Proc. Natl. Acad. Sci. USA 58, 420-427.
20. Lee, B. & Richards, F. M. (1971) J. Mol. Biol. 55, 379-400.
21. Rowlinson, J. S. (1963) Mol. Phys. 6, 517-524.
22. Pavani, R. & Ranghino, G. (1982) Comput. Chem. 6, 133-135.
23. Gavezotti, A. (1983) J. Am. Chem. Soc. 105, 5220-5225.
24. Richmond, T. J. (1984) J. Mol. Biol. 178, 63-89.
25. Connolly, M. L. (1985) J. Am. Chem. Soc. 107, 1118-1124.
26. Gibson, K. & Scheraga, H. (1987) Mol. Phys. 62, 1247-1265.
27. Petitjean, M. (1994) J. Comput. Chem. 15, 507-523.
28. Voronoi, G. F. (1908) J. Reine Angew. Math. 134, 198-287.
29. Gellatly, B. J. & Finney, J. L. (1982) J. Mol. Biol. 161, 305-322.
30. Goede, A., Preissner, R. & Frömmel, C. (1997) J. Comput. Chem. 18, 1113-1123.
31. Kratky, K. W. (1978) J. Phys. A Math. Gen. 11, 1017-1024.
32. Edelsbrunner, H. (1995) Discrete Comput. Geom. 13, 415-440.
33. Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P. V. & Subramaniam, S. (1998) Proteins Struct. Funct. Genet. 33, 1-29.
34. Kundrot, C. E., Ponder, J. W. & Richards, F. M. (1991) J. Comput. Chem. 12, 402-409.
35. Gogonea, V. & Osawa, E. (1994) J. Mol. Struct. THEOCHEM 311, 305-324.
36. Gogonea, V. & Osawa, E. (1995) J. Comput. Chem. 7, 817-842.
37. Perrot, G., Cheng, B., Gibson, K. D., Vila, J., Palmer, K. A., Nayeem, A., Maigret B. & Scheraga, H. A. (1992) J. Comput. Chem. 13, 1-11.
38. Wawak, R. J., Gibson, K. D. & Scheraga, H. A. (1994) J. Math. Chem. 15, 207-232.
39. Edelsbrunner, H. & Mücke, E. P. (1990) Am. Chem. Soc. Trans. Graphics 9, 66-104.
40. Csikós, B. (1998) Discrete Comput. Geom. 20, 449-461.
41. Edelsbrunner, H. & Shah, N. R. (1996) Algorithmica 15, 223-241.
42. Levitt, M., Hirshberg, M., Sharon, R. & Daggett, V. (1995) Comput. Phys. Common. 91, 215-231.
43. Lindahl, E., Hess, B. & van der Spoel, D. (2001) J. Mol. Mod. 7, 306-317.
44. Finney, J. L. (1975) J. Mol. Biol. 96, 721-732.