Molecular mechanics calculations of proteins. comparison of different energy minimization strategies

Journal of Biomolecular Structure and Dynamics

Volumn 15, Issue 3, 1997, Pages 473-488

  Christensen, Inge Thøger ^a   jørgensen, Flemming Steen ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; PANCREAS POLYPEPTIDE; PHOSPHOLIPASE A2;

ARTICLE; DIELECTRIC CONSTANT; ELECTRICITY; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SOLVATION; X RAY CRYSTALLOGRAPHY;

AVES; BOVINAE;

EID: 0031469242     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1997.10508959     Document Type: Article

References (47)

1. Koehler, K. F., Rao, S. N., and Snyder, J. P., 1996. Guidebook on Molecular Modeling in Drug Design Edited by:Cohen, N. C., 235–336. San Diego:Academic Press.
2. Johnson, M. S., Srinivasan, N., Sowdhamini, R., and Blundell, T. L., 1994. Crit. Rev. Biochem. Mol. Biol., 29:1–68.
3. Hutchins, C., and Greer, J., 1991. Crit. Rev. Biochem. Molec. Biol., 26:77–127.
4. Shoichet, B. K., Stroud, R. M., Santi, D. V., Kuntz, I. D., and Perry, K. M., 1993. Science, 259:1445–1450.
5. Walkinshaw, M. D., 1992. Med. Res. Rev., 12:317–372.
6. Lam, P. Y. S., Jadhav, P. K., Eyermann, C. J., Hodge, C. N., Ru, Y., Bacheler, L. T., Meek, J. L., Otto, M. J., Rayner, M. M., Wong, Y. N., Chang, C. H., Weber, P. C., Jackson, D. A., Sharpe, T. R., and Erickson-Viitanen, S., 1994. Science, 263:380–384.
7. Colman, P. M., 1994. Curr. Opin. Struct. Biol., 4:868–874.
8. Whittle, P. J., and Blundell, T. L., 1994. Annu. Rev. Biophys. Biomol. Struc., 23:349–375.
9. Bohacek, R. S., McMartin, C., and Guida, W. C., 1996. Med. Res. Rev., 16:3–50.
10. Reich, S. H., and Webber, S. E., 1993. Persp. Drug Discov. Des., 1:371–390.
11. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977. J. Mol. Biol., 112:535–542.
12. Hilbert, M., Böhm, G., and Jaenicke, R., 1993. Proteins, 17:138–151.
13. Greer, J., Erickson, J. W., Baldwin, J. J., and Varney, M. D., 1994. J. Med. Chem., 37:1035–1054.
14. Sali, A., 1995. Curr. Opin. Biotech., 6:437–451.
15. Blundell, T. L., 1996. Nature, 384:23–26.
16. Appelt, K., Bacquet, R. J., Bartlett, C. A., Booth, C. L. J., Freer, S. T., Fuhry, M. A. M., Gehring, M. R., Herrmann, S. M., Howland, E. F., Janson, C. A., Jones, T. R., Kan, C-C., Kathardekar, V., Lewis, K. K., Marzoni, G. P., Matthews, D. A., Mohr, C., Moomaw, E. W., Morse, C. A., Oatley, S. J., Ogden, R. C., Reddy, M. R., Reich, S. H., Schoettlin, W. S., Smith, W. W., Varney, M. D., Villafranca, J. E., Ward, R. W., Webber, S., Webber, S. E., Welsh, K. M., and White, J., 1991. J. Med. Chem., 34:1925–1934.
17. Goodsell, D. S., and Olson, A. J., 1990. Proteins, 8:195–202.
18. Leach, A. R., 1994. J. Mol. Biol., 235:345–356.
19. Kuntz, I. D., Meng, E. C., and Shoichet, B. K., 1994. Acc. Chem. Res., 27:117–123.
20. Blaney, J. M., and Dixon, J. S., 1993. Persp. Drug Discov. Des., 1:301–319.
21. Straatsma, T. P., Zacharias, M., and McCammon, J. A., 1993. Computer Simulation of Biomolecular Systems. Theoretical and Experimental Applications. Vol. Edited by:van Gunsteren, W. F., Weiner, P. K., and Wilkinson, A. J., Vol. 2, 349–367. Leiden:ESCOM Science Publishers B.V. by
22. Dijkstra, B. W., Kalk, K. H., Hol, W. G. J., and Drenth, J., 1981. J. Mol. Biol., 147:97–123.
23. Blundell, T. L., Pitts, J. E., Tickle, I. J., Wood, S. P., and Wu, C.-W., 1981. Proc. Natl. Acad. Sci. USA., 78:4175–4179.
24. Fremont, D. H., Anderson, D. H., Wilson, I. A., Dennis, E. A., and Xuong, N.-H., 1993. Proc. Natl. Acad. Sci. USA, 90:342–346.
25. Modin, C. R., Christensen, I. T., and Jørgensen, F. S., in preparation
26. Tripos Associates Inc., St. Louis, USA
27. Labanowski, J., Motoc, I., Naylor, C. B., Mayer, D., and Dammkoehler, R. A., 1986. Quant. Struct.-Act. Relat., 5:138–152.
28. Clark, M., Cramer, R. D., III and Van Opdenbosch, N., 1989. J. Comput. Chem., 10:982–1012.
29. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., 1986. J. Comput. Chem., 7:230–252.
30. Teeter, M. M., 1991. Annu. Rev. Biophys. Biophys. Chem., 20:577–600.
31. Blanco, M., 1991. J. Comput. Chem., 12:237–247.
32. Stewart, J. J. P., 1990. J. Comput.-Aided. Mol. Des., 4:1–105.
33. Pearlman, R. S., and Skell, J. M., SAVOL3:Numerical and Analytical Algorithms for Molecular Surface Area and Volume, software distributed by R. S. Pearlman 78712Austin TX:College of Pharmacy, University of Texas.
34. Morris, A. L., MacArthur, M. W., Hutchinson, E. G., and Thornton, J. M., 1992. Proteins, 12:345–364.
35. Kini, R. M., and Evans, H. J., 1991. J. Biomol. Struct. Dyn., 9:475–488.
36. Shiratori, Y., and Nakagawa, S., 1991. J. Comput. Chem., 12:717–730.
37. Thrige, D. d. G., Buur, J. R. B., and Jørgensen, F. S., 1997. Biopolymers, 42:319–336.
38. Christensen, I. T., Jørgensen, F. S., Svensson, Å. L., and Högberg, T., 1993. Drug Des. Discov., 10:101–113.
39. Keith, C., Feldman, D. S., Deganello, S., Glick, J., Ward, K. B., Jones, E. O., and Sigler, P. B., 1981. J. Biol. Chem., 256:8602–8607.
40. Christensen, I. T., and Jørgensen, F. S., unpublished results
41. Weiner, P. K., Langridge, R., Blaney, J. M., Schaefer, R., and Kollman, P. A., 1982. Proc. Natl. Acad. Sci. USA., 79:3754–3758.
42. von Freyberg, B., Richmond, T. J., and Braun, W., 1993. J. Mol. Biol., 233:275–292.
43. Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrickson, T. F., 1990. J. Am. Chem. Soc., 112:6127–6129.
44. Schiffer, C. A., Caldwell, J. W., Kollman, P. A., and Stroud, R. M., 1993. Mol. Simul., 102:121–149.
45. Stouten, P. F. W., Frömmel, C., Nakamura, H., and Sander, C., 1993. Mol. Simul., 102:97–120.
46. Scott, D. L., White, S. P., Otwinowski, Z., Yuan, W., Gelb, M. H., and Sigler, P. B., 1990. Science, 250:1541–1546.
47. Kraulis, P. J., 1991. J. Appl. Cryst., 24:946–950.