Protein structure prediction by global optimization of a potential energy function

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

Volumn 96, Issue 10, 1999, Pages 5482-5485

  Liwo, Adam ^a,b   Lee, Jooyoung ^a   Ripoll, Daniel R ^a   Pillardy, Jaroslaw ^a   Scheraga, Harold A ^a  

^a Cornell University ^*  (United States)

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ENERGY TRANSFER; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 0033545962     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.96.10.5482     Document Type: Article

References (52)

1. Lewis, P. N. & Scheraga, H. A. (1971) Arch. Biochem. Biophys. 144, 584-588.
2. Warme, P. K., Momany, F. A., Rumball, S. V., Tuttle, R. W. & Scheraga, H. A. (1974) Biochemistry 13, 768-782.
3. Jones, T. A. & Thirup, S. (1986) EMBO J. 5, 819-822.
4. Clark, D. A., Shirazi, J. & Rawlings, C. J. (1991) Prot. Eng. 4, 751-760.
5. Rooman, M. J. & Wodak, S. J. (1992) Biochemistry 31, 10239-10249.
6. Johnson, M. S., Overington, J. P. & Blundell, T. L. (1993) J. Mol. Biol. 231, 735-752.
7. Scheraga, H. A. (1992) Int. J. Quant. Chem. 42, 1529-1536.
8. Scheraga, H. A. (1996) Biophys. Chem. 59, 329-339.
9. Vásquez, M., Némethy, G. & Scheraga, H. A. (1994) Chem. Rev. 94, 2183-2239.
10. Anfinsen, C. B. (1973) Science 181, 223-230.
11. Fischer, D., Rice, D., Bowie, J. U. & Eisenberg, D. (1996) FASEB J. 10, 126-136.
12. Jones, D. T. (1997) Curr. Opin. Struct. Biol. 7 377-387.
13. Mirny, L. A. & Shakhnovich, E. I. (1998) J. Mol. Biol. 283, 507-526.
14. Skolnick, J., Koliński, A., Brooks III, C. L., Godzik, A. & Rey, A. (1993) Curr. Biol. 3, 414-424.
15. Koliński, A. & Skolnick, J. (1994) Proteins Struct. Funct. Genet. 18, 338-352.
16. Skolnick, J., Koliński, A. & Ortiz, A. R. (1997) J. Mol. Biol. 265, 217-241.
17. Reva, B. A., Finkelstein, A. V. & Skolnick, J. (1998) Fold. Des. 3, 141-147.
18. Dill, K. A. (1990) Biochemistry 29, 7133-7155.
19. Goldstein, R. A., Luthey-Schulten, Z. A. & Wolynes, P. G. (1992) Proc. Natl. Acad. Sci. USA 89, 9029-9033.
20. Sǎli, A., Shakhnovich, E. & Karplus, M. (1994) Nature (London) 369, 248-251.
21. Hao, M. H. & Scheraga, H. A. (1994) J. Phys. Chem. 98, 9882-9893.
22. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. (1995) Science 267, 1619-1620.
23. Hao, M. H. & Scheraga, H. A. (1995) J. Chem. Phys. 102, 1334-1348.
24. Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1993) Protein Sci. 2, 1697-1714.
25. Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1993) Protein Sci. 2, 1715-1731.
26. Levitt, M. & Warshel, A. (1975) Nature (London) 253, 694-698.
27. Seetharamulu, P. & Crippen, G. M. (1991) J. Math. Chem. 6, 91-110.
28. Maiorov, V. N. & Crippen, G. M. (1992) J. Mol. Biol. 227, 876-888.
29. Liwo, A., Oldziej, S., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1997) J. Comput. Chem. 18, 849-873.
30. Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S., Oldziej, S. & Scheraga, H. A. (1997) J. Comput. Chem. 18, 874-887.
31. Liwo, A., Kaźmierkiewicz, R., Czaplewski, C., Groth, M., Oldziej, S., Wawak, R. J., Rackovsky, S., Pincus, M. R. & Scheraga, H. A. (1998) J. Comput. Chem. 19, 259-276.
32. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977) J. Mol. Biol. 112, 535-542.
33. Hao, M. H. & Scheraga, H. A. (1996) Proc. Natl. Acad. Sci. USA 93, 4984-4989.
34. Hao, M. H. & Scheraga, H. A. (1996) J. Phys. Chem. 100, 14540-14584.
35. Lee, J., Scheraga, H. A. & Rackovsky, S. (1997) J. Comput. Chem. 18, 1222-1232.
36. Lee, J., Scheraga, H. A. & Rackovsky, S. (1998) Biopolymers 46, 103-115.
37. Lee, J., Liwo, A. & Scheraga, H. A. (1999) Proc. Natl. Acad. Sci. USA, 96, 2025-2030.
38. Lee, J. & Scheraga, H. A. (1999) Int. J. Quant. Chem., in press.
39. Goldberg, D. E. (1989) Genetic Algorithms in Search, Optimization and Machine Learning. (Addison-Wesley, Reading, MA).
40. Ripoll, D. R. & Scheraga, H. A. (1988) Biopolymers 27, 1283-1303.
41. Ripoll, D. R. & Scheraga, H. A. (1990) Biopolymers 30, 165-176.
42. Ripoll, D. R., Liwo, A. & Scheraga, H. A. (1998) Biopolymers 46, 117-126.
43. Gö, N. & Scheraga, H. A. (1970) Macromolecules 3, 178-187.
44. Palmer, K. A. & Scheraga, H. A. (1991) J. Comput. Chem. 12, 505-526.
45. Momany, F. A., McGuire, R. F., Burgess, A. W. & Scheraga, H. A. (1975) J. Phys. Chem. 79, 2361-2381.
46. Némethy, G., Pottle, M. S. & Scheraga, H. A. (1983) J. Phys. Chem. 87, 1883-1887.
47. Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S. & Scheraga, H. A. (1992) J. Phys. Chem. 96, 6472-6484.
48. Vila, J., Williams, R. L., Vásquez, M. & Scheraga, H. A. (1991) Proteins Struct. Funct. Genet. 10, 199-218.
49. Lee, J., Liwo, A., Ripoll, D. R., Pillardy, J. & Scheraga, H. A. (1999) Proteins Struct. Funct. Genet., submitted.
50. Yang, F., Gustafson, K. R., Boyd, M. R. & Wlodawer, A. (1998) Nat. Struct. Biol. 5, 763-764.
51. Koehl, P. & Levitt, M. (1999) Nat. Struct. Biol. 6, 108-111.
52. Rhee, S., Martin, R. G., Rosner, J. L. & Davies, D. R. (1998) Proc. Natl. Acad. Sci. USA 95, 10413-10418.