A global optimization strategy for predicting α-helical protein tertiary structure

Computers and Chemistry

Volumn 24, Issue 3-4, 2000, Pages 489-497

  Crivelli, Silvia ^a   Byrd, Richard ^b   Eskow, Elizabeth ^b   Schnabe, Robert ^b   Yu, Richard ^a,c   Philip, Thomas M ^a   Head Gordon, Teresa ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UCB 450   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

Conformational search; Constraint optimization; Energy functions; Hydrophobic effect; Parallelization

Indexed keywords

DNA BINDING PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PHYSICAL CHEMISTRY; PREDICTION AND FORECASTING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PREDICTIVE VALUE OF TESTS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 0034186484     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(99)00087-X     Document Type: Article

References (44)

1. Assa-Munt, N., Mortishire-Smith, R.J., Aurora, R., Herr, W., Wright, P.E., 1993. Cell 73, 193.
2. Azmi, A., Byrd, R.H., Eskow, E., Schnabel, R., Crivelli, S., Philip, T.M., Head-Gordon, T., 1999. International conference on optimization in computational chemistry and molecular biology: local and global approaches, accepted for publication.
3. Bally, R., Delettre, J., 1984. J. Mol. Biol. 206, 153.
4. Byrd, R.H., Eskow, E., Oldenkamp, B., Schnabel, R.B., van der Hoek, A., 1995a. In: Proceedings of the Seventh SIAM Conference on Parallel Processing for Scientific Computing, SIAM, pp. 72-77.
5. Byrd, R., Eskow, E., van der Hoek, A., Schnabel, R., Shao, C.-S., Zou, Z., 1995b. In: Pardalos, P., Shalloway, D., Xue, G. (Eds.), Proceedings of the DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, American Mathematical Society.
6. Byrd, R.H., Derby, T., Eskow, E., Oldenkamp, K.P.B., Schnabel, R.B., 1994. Large-Scale Optimization. In: Hager, W., Hearn, D., Pardalos, P. (Eds.), State Of The Art. Kluwer Academic Publishers, Dordrecht, pp. 71-84.
7. Cornell, W.D., Cieplak, P., Bayly, C.I., et al., 1995. J. Am. Chem. Soc. 117, 5179.
8. Crivelli, S., Gordon,T., Byrd, R.H.,Lecture Notes in Computer Science. In; Amestoy, P., Berger, P., Dayde, M., Duff, I., Fraysse, V., Giraud, L., Ruiz, D. (Eds.),Europar '99. pp. 578-585
9. Crivelli, S., Head-Gordon, T., 1999. J. Parallel Comput..submitted.
10. Eisenhaber, F., Persson, B., Argos, P., 1995. Crit. Rev. Biochem. Mol. Biol. 30, 1.
11. Friesner, R.A., Gunn, Jr., 1996. Ann. Rev. Biophys. Biomol. Struct. 25, 315.
12. Gay, D.M., Head-Gordon, T., Stillinger, F.H., Wright, M.H., 1992. Forefronts. Corn. Theory Center 8, 4.
13. Head-Gordon, T., Arrecis, J., Stillinger, F.H., 1991. Proc. Natl. Acad. Sci. USA 88, 11076.
14. Head-Gordon, T., Stillinger, F.H., Wright, M.H., Gay, D.M., 1992. Proc. Natl. Acad. Sci. USA 89, 11513.
15. Head-Gordon, T., Stillinger, F.H., 1993a. Biopolymers 33, 293.
16. Head-Gordon, T., Stillinger, F.H., 1993b. Phys. Rev. E. 48, 1502.
17. Head-Gordon, T., 1996. In: Merz, K.M., Le Grand, S.M. (Eds.), The Protein Folding Problem and Tertiary Structure Prediction. Birkhauser, Boston.
18. Head-Gordon, T., 1995. J. Am. Chem. Soc. 117, 501.
19. Head-Gordon, T., Sorenson, J.M., Pertsemlidis, A., Glaeser, R.M., 1997. Biophys. J. 73, 2106.
20. Holley, L.H., Karplus, M., 1991. Methods Enzym. 202, 204.
21. Hura, G., Sorenson, J.M., Glaeser, R.M., Head-Gordon, T., 1999. Perspectives in Drug Discovery, in press.
22. Kneller, D.G., Cohen, F.E., Langridge, R., 1990. J. Mol. Biol. 214, 171.
23. Liu, D.C., Nocedal, J., 1989. Math. Program. 45, 503.
24. Lovasz, L., Plummer, M.D., 1986. Matching Theory. Elsevier, Amsterdam.
25. McGregor, M.J., Flores, T.P., Sternberg, M.J.E., 1989. Protein Eng. 2, 521.
26. Muskal, S.M., Kim, S.-H., 1992. J. Mol. Biol. 225, 713.
27. Novotny, J., Bruccoleri, R., Karplus, M., 1984. J. Mol. Biol. 177, 787.
28. Pertsemlidis, A., Saxena, A.M., Soper, A.K., Head-Gordon, T., Glaeser, R.M., 1996. Proc. Natl. Acad. Sci. 93, 10769.
29. Pertsemlidis, A., Soper, A.K., Sorenson, J.M., Head-Gordon, T., 1999. Proc. Natl. Acad. Sci. 96, 481.
30. Pratt, L.R., Chandler, D., 1977. J. Chem. Phys. 67, 3683.
31. Pratt, L.R., Chandler, D., 1980. J. Chem. Phys. 73, 3434.
32. Qian, N., Sejnowski, T.J., 1988. J. Mol. Biol. 202, 865.
33. Rick, S.W., Berne, B.J., 1997. J. Phys. Chem. B. 101, 10488.
34. Rinnooy-Kan, A.H.G., Timmer, G., 1984. In: Boggs, P., Byrd, R., Schnabel, R.B. (Eds.), Numerical Optimization. SIAM, Philadelphia, pp. 245-262.
35. Rost, B., Sander, C., 1994. Proteins 19, 55.
36. Schiffer, C.A., Caldwell, J.W., Kollman, P.A., Stroud, R.M., 1993. Mol. Simul. 10, 121-149.
37. Sorenson, J.M., Head-Gordon, T., 1998. Fold. Des. 3, 523-534.
38. Sorenson, J.M., Hura, G., Pertsemlidis, A., Soper, A.K., Head-Gordon, T., 1999. J. Phys. Chem. B. 103, 5413.
39. Stillinger, F.H., Head-Gordon, T., Hirshfeld, C.L., 1993. Phys. Rev. E. 48, 1469.
40. Szebenyi, D.M.E., Moffat, K., 1986. J. Biol. Chem. 261, 8761.
41. Vasquez, M., Nemethy, G., Scheraga, H.A., 1994. Chem. Rev. 94, 2183.
42. Wesson, L., Eisenberg, D., 1992. Protein Science 1, 227-235.
43. Yu, R.C., Head-Gordon, T., 1995. Phys. Rev. E. 51, 3619.
44. Zichi, D.A., Rossky, P.J., 1985. J. Chem. Phys. 83, 797.