Protein design based on the relative entropy

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 73, Issue 6, 2006, Pages

  Jiao, Xiong ^a   Wang, Baohan ^b   Su, Jiguo ^a   Chen, Weizu ^a   Wang, Cunxin ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ITERATIVE METHODS; MATHEMATICAL MODELS; OPTIMIZATION; PROTEINS; STRUCTURAL DESIGN;

INVERSE FOLDING; OFF-LATTICE MODELS; PROTEIN DESIGN; RELATIVE ENTROPY;

ENTROPY;

EID: 33744802957     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.73.061903     Document Type: Article

References (28)

1. J. M. Deutsch and T. Kurosky, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.76.323 76, 323 (1996).
2. K. Yue and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 89, 4163 (1992).
3. M. P. Morrissey and E. I. Shakhnovich, Folding Des. FODEFH 1359-0278 1, 391 (1996).
4. S. Miyazawa and R. L. Jernigan, Macromolecules MAMOBX 0024-9297 10.1021/ma00145a039 18, 534 (1985).
5. S. Miyazawa and R. L. Jernigan, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0114 256, 623 (1996).
6. J. G. Saven, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr000058w 101, 3113 (2001).
7. F. Seno, M. Vendruscolo, A. Maritan, and J. R. Banavar, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.77.1901 77, 1901 (1996).
8. E. I. Shakhnovich and A. M. Gutin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 90, 7195 (1993).
9. E. I. Shakhnovich and A. M. Gutin, Protein Eng. PRENE9 0269-2139 6, 793 (1993).
10. E. I. Shakhnovich, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett. 72.3907 72, 3907 (1994).
11. J. Desmet, M. Demaeyer, B. Hazes, and I. Lasters, Nature (London) NATUAS 0028-0836 10.1038/356539a0 356, 539 (1992).
12. B. Dahiyat and S. L. Mayo, Protein Sci. PRCIEI 0961-8368 5, 895 (1996).
13. B. Dahiyat, C. A. Sarisky, and S. L. Mayo, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1997.1341 273, 789 (1997).
14. P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science SCIEAS 0036-8075 10.1063/1.471317 267, 1619 (1995).
15. N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.471317 104, 5860 (1996).
16. K. A. Dill, Biochemistry BICHAW 0006-2960 10.1021/bi00327a032 24, 1501 (1985);
17. K. F. Lau and K. A. Dill, Macromolecules MAMOBX 0024-9297 10.1021/ma00200a030 22, 3986 (1989).
18. E. I. Shakhnovich, Folding Des. FODEFH 1359-0278 3, 45 (1998).
19. E. I. Shakhnovich, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett. 72.3907 72, 3907 (1994).
20. A. Rossi, C. Micheletti, F. Seno, and A. Maritin, Biophys. J. BIOJAU 0006-3495 80, 480 (2001).
21. B. Z. Lu, B. H. Wang, W. Z. Chen, and C. X. Wang, Protein Eng. PRENE9 0269-2139 16, 695 (2003).
22. Y. Liu, B. H. Wang, C. X. Wang, and W. Z. Chen, Sci. China, Ser. G SCSGCI 1672-1799 46, 659 (2003).
23. Y. H. Wang, B. H. Wang, Y. Liu, W. Z. Chen, and C. X. Wang, Chin. Sci. Bull. CSBUEF 1001-6538 49, 5 (2004).
24. B. Kull and R. A. Leibler, Ann. Math. Stat. AASTAD 0003-4851 22, 79 (1951).
25. T. P. Li, K. Fan, J. Wang, and W. Wang, Protein Eng. PRENE9 0269-2139 16, 323 (2003).
26. V. N. Maiorov and G. M. Crippen, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(92)90228-C 227, 876 (1992).
27. C. Micheletti, F. Seno, A. Maritan, and J. R. Banavar, Proteins 18PLAF 0887-3585 10.1002/(SICI)1097-0134(19980701)32:1<80::AID-PROT9>3.0.CO;2-I 32, 80 (1998).
28. C. Chothia and A. M. Lesk, EMBO J. EMJODG 0261-4189 5, 823 (1986).