A flexible triangulation method to describe the solvent-accessible surface of biopolymers

Journal of Computer-Aided Molecular Design

Volumn 12, Issue 3, 1998, Pages 289-299

  Juffer, André H ^a   Vogel, Hans J ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

Boundary element method; Continuum electrostatics; Solvent accessible surface; Triangulation

Indexed keywords

BOUNDARY ELEMENT METHOD; C++ (PROGRAMMING LANGUAGE); COMPUTER SOFTWARE; DISSOCIATION; MOLECULES; PEPTIDES; SAILING VESSELS; SOLVENTS;

BOUNDARY-ELEMENT METHODS; CONTINUUM ELECTROSTATIC; ELECTROSTATIC APPLICATION; LATTICE POINTS; LATTICE SPACING; SIMPLE++; SOLVENT-ACCESSIBLE SURFACES; SURFACE TRIANGULATION; THREE-DIMENSIONAL LATTICES; TRIANGULATION METHOD;

ELECTROSTATICS;

BIOPOLYMER; CALMODULIN; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY;

BIOPOLYMERS; CALMODULIN; MODELS, MOLECULAR; SOLVENTS;

EID: 0032059253     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1016089901704     Document Type: Article

References (50)

1. Harvey, S., Proteins Struct. Fund. Genet., 5 (1989) 78.
2. Davids, M.E. and McCammon, J.A., Chem. Rev., 90 (1990) 509.
3. Mantripragada, B. and March, D., In Watts, A. (Ed.) Protein-Lipid Interactions, Elsevier, Amsterdam, 1993, pp. 127-162.
4. Warwicker, J. and Watson, H.C., J. Mol. Biol., 157 (1982) 671.
5. Bashford, D. and Karplus, M., Biochemistry, 29 (1990) 10219.
6. Zauhar, R.J. and Morgan, R.S., J. Mol. Biol., 186 (1985) 815.
7. Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 9 (1988) 171.
8. Rashin, A.A., J. Phys. Chem., 94 (1990) 1725.
9. Yoon, B.J. and Lenhoff, A.M., J. Comput. Chem., 11 (1990) 1080.
10. Juffer, A.M., Botta, E.F.F., van Keulen, B.A.M., van der Ploeg, A. and Berendsen, H.J.C., J. Comput. Phys., 97 (1991) 144.
11. Bharadwaj, R., Windemuth, A., Sridharan, S., Honig, B. and Nicholls, A., J. Comput. Chem., 16 (1995) 898.
12. Sanner, M.F., Olson, A.J. and Spehner, J.-C., Biopolymers, 38 (1996) 305.
13. Zauhar, R.J., J. Comput.-Aided Mol. Design, 9 (1995) 149.
14. Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 11 (1990) 603.
15. Connolly, M.L., J. Appl. Crystallogr., 18 (1985) 499.
16. Connolly, M.L., J. Mol. Graphics, 11 (1993) 139.
17. Silla, E., Villar, F., Nilsson, O., Pascual-Ahuir, J.L. and Tapia, O., J. Mol. Graphics, 8 (1990) 168.
18. Zhexin, X., Yunyu, S. and Yingwu, X., J. Comput. Chem., 16 (1995) 512.
19. Stollnitz, E.J., DeRose, T.D. and Salesin, D.H., IEEE Comput. Graph. Appl., 15(3) (1995) 76.
20. Stollnitz, E.J., DeRose, T.D. and Salesin, D.H., IEEE Comput. Graph. Appl., 15(4) (1995) 75.
21. Duncan, B.S. and Olson, A.J., Biopolymers, 33 (1993) 219.
22. Timchenko, A.A., Galzitskaya, O.V. and Serdyuk, I.N., Proteins Struct. Funct. Genet., 28 (1997) 194.
23. Certain, A., Popovic, J., DeRose, T., Duchamp, T., Salesin, D. and Stuezle, W, In Proceedings of SIGGRAPH 96, ACM SIGGRAPH, New Orleans, p. 91.
24. Hoppe H., In Proceedings of SIGGRAPH 96, ACM SIGGRAPH, New Orleans, p. 99.
25. Cohen, J., Varshney, A., Manocha, D., Turk, G., Weber, H., Agarwal, P., Brooks, F. and Wright, W., In Proceedings of SIGGRAPH 96, ACM SIGGRAPH, New Orleans, p. 119.
26. Hoppe, H., In Proceedings of SIGGRAPH 97, ACM SIGGRAPH, Los Angeles, p. 189.
27. Luebke, D. and Erikson, C., In Proceedings of SIGGRAPH 97, ACM SIGGRAPH, Los Angeles, p. 199.
28. Garland, M. and Heckbert, P., In Proceedings of SIGGRAPH 97, ACM SIGGRAPH, Los Angeles, p. 209.
29. Popovic, J. and Hoppe, H., In Proceedings of SIGGRAPH 97, ACM SIGGRAPH, Los Angeles, p. 217.
30. Akkiraju, N. and Edelsbrunner, H., Discrete Appl. Math., 71 (1996) 5.
31. Lorensen, W.E. and Cline, H.E., Comput. Graphics, 21 (1987) 163.
32. Lee, B. and Richards, F.M., J. Mol. Biol., 55 (1971) 379.
33. Vogel, H.J., Biochem. Cell Biol., 72 (1995) 357.
34. Juffer, A.H., Argos, P. and Vogel, H.J., J. Phys. Chem., 101 (1997) 7664.
35. Ban, C., Ramakrishnan, B., Ling, K-.Y., Kung, C. and Sundaralingam, M., Acta Crystallogr., D50 (1994) 50.
36. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.P., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
37. Babu, Y.S., Sack, J.S., Greenbrough, T.J., Bugg, C.E., Means, A.R. and Cook, W.J., Nature, 315 (1985) 37.
38. Babu, Y.S., Bugg, C.E. and Cook, W.J., J. Mol. Biol., 204 (1988) 191.
39. Eisenhaber, F. and Argos, P., J. Comput. Chem., 14 (1993) 1272.
40. Eisenhaber, E, Lijnzaad, P., Argos, P., Sander, C. and Scharf, M., J. Comput. Chem., 16 (1995) 273.
41. Szabenyi, D.M.E. and Moffat, K., J. Biol. Chem., 261 (1986) 8761.
42. Hodson, J.M., Brown, G.M. and Sieker, L.C., Acta Crystallogr. B46 (1990) 54.
43. Martinez, C., De Geus, P., Lauwereys, M. and Matthyssens, G., Nature, 356 (1992) 616.
44. Vriend, G., J. Mol. Graphics, 8 (1990) 52.
45. Insight II, version 95.0, October 1995, Biosym/MSI, San Diego, CA.
46. van der Spoel, D., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., van Druunen, R. and Berendsen, H.J.C., Gromacs User Manual, State University of Groningen, 1996.
47. Zauhar, R.J. and Varnek, A., J. Comput. Chem., 17 (1996) 864.
48. Honig, B., Sharp, K. and Yang, A.-S., J. Phys. Chem., 97 (1993) 1101.
49. Hubbard, S.J. and Argos, P., Curr. Opin. Biotech., 6 (1995) 375.
50. Hubbard, S.J. and Argos, P., J. Mol. Biol., 261 (1996) 289.