Using protein design for homology detection and active site searches

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

Volumn 100, Issue 20, 2003, Pages 11361-11366

  Pei, Jimin ^a   Dokholyan, Nikolay V ^c,d   Shakhnovich, Eugene I ^c   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYPEPTIDASE A; LYSOZYME; RHO FACTOR; RIBONUCLEASE; TRYPSIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ENERGY TRANSFER; MOLECULAR EVOLUTION; MOLECULAR MODEL; MONTE CARLO METHOD; PHYLOGENY; PRIORITY JOURNAL; PROTEIN STABILITY; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; Z SCORE;

BINDING SITES; EVOLUTION, MOLECULAR; MODELS, CHEMICAL; PROTEINS;

ARTIFICIAL SEQUENCES;

EID: 0141705410     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2034878100     Document Type: Article

References (37)

1. Shakhnovich, E. I. & Gutin, A. M. (1993) Protein Eng. 6, 793-800.
2. Shakhnovich, E. I. (1998) Folding Des. 3, R45-R58.
3. DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F. & Lombardi, A. (1999) Annu. Rev. Biochem. 68, 779-819.
4. Pokala, N. & Handel, T. M. (2001) J. Struct. Biol. 134, 269-281.
5. Dahiyat, B. I. & Mayo, S. L. (1997) Science 278, 82-87.
6. Kuhlman, B. & Baker, D. (2000) Proc. Natl. Acad. Sci. USA 97, 10383-10388.
7. Koehl, P. & Levitt, M. (2002) Proc. Natl. Acad. Sci. USA 99, 1280-1285.
8. Koehl, P. & Levitt, M. (2002) Proc. Natl. Acad. Sci. USA 99, 691-696.
9. Raha, K., Wollacott, A. M., Italia, M. J. & Desjarlais, J. R. (2000) Protein Sci. 9, 1106-1119.
10. Dokholyan, N. V. & Shakhnovich, E. I. (2001) J. Mol. Biol. 312, 289-307.
11. Sippl, M. J. (1990) J. Mol. Biol. 213, 859-883.
12. Miyazawa, S. & Jernigan, R. L. (1999) Proteins 34, 49-68.
13. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
14. Shakhnovich, E. I. & Gutin, A. M. (1993) Proc. Natl. Acad. Sci. USA 90, 7195-7199.
15. Schultz, J., Copley, R. R., Doerks, T., Ponting, C. P. & Bork, P. (2000) Nucleic Acids Res. 28, 231-234.
16. Pei, J. & Grishin, N. V. (2001) Bioinformatics 17, 700-712.
17. Walker, D. R. & Koonin, E. V. (1997) Intelligent Syst. Mol. Biol. 5, 333-339.
18. Notredame, C., Higgins, D. G. & Heringa, J. (2000) J. Mol. Biol. 302, 205-217.
19. Henikoff, S. & Henikoff, J. G. (1994) J. Mol. Biol. 243, 574-578.
20. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978) in Atlas of Protein Sequences and Structures, ed. Dayhoff, M. O. (National Biomedical Research Foundation, Washington, DC), Vol. 5, Suppl. 3, pp. 345-352.
21. Murzin, A. G. (1993) EMBO J. 12, 861-867.
22. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995) J. Mol. Biol. 247, 536-540.
23. Schindelin, H., Jiang, W., Inouye, M. & Heinemann, U. (1994) Proc. Natl. Acad. Sci. USA 91, 5119-5123.
24. Grishin, V. N. & Grishin, N. V. (2002) Bioinformatics 18, 1523-1534.
25. Shoichet, B. K., Baase, W. A., Kuroki, R. & Matthews, B. W. (1995) Proc. Natl. Acad. Sci. USA 92, 452-456.
26. Adell, J. C. & Dopazo, J. (1994) J. Mol. Evol. 38, 305-309.
27. Feng, D. F. & Doolittle, R. F. (1997) J. Mol. Evol. 44, 361-370.
28. Grishin, N. V. (1995) J. Mol. Evol. 41, 675-679.
29. Dunbrack, R. L., Jr., & Karplus, M. (1993) J. Mol. Biol. 230, 543-574.
30. Panchenko, A. R., Marchler-Bauer, A. & Bryant, S. H. (2000) J. Mol. Biol. 296, 1319-1331.
31. Xu, Y. & Xu, D. (2000) Proteins 40, 343-354.
32. Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225.
33. Voigt, C. A., Gordon, D. B. & Mayo, S. L. (2000) J. Mol. Biol. 299, 789-803.
34. Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987) Proc. Natl. Acad. Sci. USA 84, 4355-4358.
35. Eddy, S. R. (1998) Bioinformatics 14, 755-763.
36. Abbott, J. J., Pei, J., Ford, J. L., Qi, Y., Grishin, V. N., Pitcher, L. A., Phillips, M. A. & Grishin, N. V. (2001) J. Biol. Chem. 276, 42099-42107.
37. Guindon, S. & Gascuel, O. (2002) Mol. Biol. Evol. 19, 534-543.