Coupled prediction of protein secondary and tertiary structure

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

Volumn 100, Issue 21, 2003, Pages 12105-12110

  Meiler, Jens ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Artificial neural networks; CASP; Fragment replacement; Protein folding; ROSETTA

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 0142027795     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1831973100     Document Type: Article

References (58)

1. Garnier, J., Osguthorpe, D. J. & Robson, B. (1978) J. Mol. Biol. 120, 97-120.
2. Schulz, G. E., Barry, C. D., Friedman, J., Chou, P. Y., Fasman, G. D. Finkelstein, A. V., Lim, V. I., Pititsyn, O. B., Kabat, E. A., Wu, T. T., et al. (1974) Nature 250, 140-142.
3. Pain, R. H. & Robson, B. (1970) Nature 227, 62-63.
4. Qian, N. & Sejnowski, T. J. (1988) J. Mol. Biol. 202, 865-884.
5. Kneller, D. G., Cohen, F. E. & Langridge, R. (1990) J. Mol. Biol. 214, 171-182.
6. Rost, B., Sander, C. & Schneider, R. (1994) J. Mol. Biol. 235, 13-26.
7. Chandonia, J.-M. & Karplus, M. (1995) Protein Sci. 4, 275-285.
8. Vivarelli, F., Giusti, G., Villani, M., Campanini, R., Fariselli, P., Compiani, M. & Casadio, R. (1995) Comput. Appl. Biosci. 11, 253-260.
9. King, R. D. & Sternberg, M. J. E. (1996) Protein Sci. 5, 2298-2310.
10. Chandonia, J.-M. & Karplus, M. (1999) Proteins Struct. Funct. Genet. 35, 293-306.
11. Selbig, J., Mevissen, T. & Lengauer, T. (1999) Bioinformatics 15, 1039-1046.
12. Petersen, T. N., Lundegaard, C., Nielsen, M., Bohr, H., Bohr, J., Brunak, S., Gippert, G. P. & Lund, O. (2000) Proteins Struct. Funct. Genet. 41, 17-20.
13. Meiler, J., Müller, M., Zeidler, A. & Schmäschke, F. (2001) J. Mol. Model. 7, 360-369.
14. Rost, B. & Sander, C. (1993) J. Mol. Biol. 232, 584-599.
15. Rost, B. & Sander, C. (1993) Proc. Natl. Acad. Sci. USA 90, 7558-7562.
16. Jones, D. T. (1999) J. Mol. Biol. 292, 195-202.
17. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410.
18. Bystroff, C., Thorsson, V. & Baker, D. (2000) J. Mol. Biol. 301, 173-190.
19. de la Cruz, X., Hutchinson, E. G., Shepherd, A. & Thornton, J. M. (2002) Proc. Natl. Acad. Sci. USA 99, 11157-11162.
20. Kuhn, M., Meiler, J. & Baker, D. (2003) Proteins, in press.
21. Kolinski, A., Skolnick, J., Godzik, A. & Hu, W.-P. (1997) Proteins Struct. Funct. Genet. 27, 290-308.
22. Hu, W.-P., Kolinski, A. & Skolnick, J. (1997) Proteins 29, 443-460.
23. Scheraga, H. A. & Montelione, G. T. (1989) Acc. Chem. Res. 22, 70-76.
24. Reymond, M. T., Merutka, G., Dyson, H. J. & Wright, P. E. (1997) Protein Sci. 6, 706-716.
25. Blanco, F. J., Rivas, G. & Serrano, L. (1994) Nat. Struct. Biol. 1, 584-590.
26. Ramirez-Alvarado, M., Serrano, L. & Blanco, F. J. (1997) Protein Sci. 6, 162-174.
27. Sanz, J. M., Jimenez, M. A. & Gimenez-Gallego, G. (2002) Biochemistry 41, 1923-1933.
28. Luisi, D. L., Wu, W. J. & Raleigh, D. P. (1999) J. Mol. Biol. 287, 395-407.
29. Cregut, D., Civera, C., Macias, M. J., Wallon, G. & Serrano, L. (1999) J. Mol. Biol. 292, 389-401.
30. Callihan, D. E. & Logan, T. M. (1999) J. Mol. Biol. 285, 2161-2175.
31. Kuroda, Y., Hamada, D., Tanaka, T. & Goto, Y. (1996) Folding Des. 1, 255-263.
32. Cerpa, R., Cohen, F. E. & Kuntz, I. D. (1996) Folding Des. 1, 91-101.
33. Hamada, D., Kuroda, Y., Tanaka, T. & Goto, Y. (1995) J. Mol. Biol. 254, 737-746.
34. Minor, D. L., Jr., & Kim, P. S. (1996) Nature 380, 730-734.
35. Pan, K. M., Baldwin, M., Nguyen, J., Gasset, M., Serban, A., Groth, D., Mehlhorn, I., Huang, Z., Fletterick, R. J., Cohen, F. E., et al. (1993) Proc. Natl. Acad. Sci. USA 90, 10962-10966.
36. Cohen, F. E., Pan, K. M., Huang, Z., Baldwin, M., Fletterick, R. J. & Prusiner, S. B. (1994) Science 264, 530-531.
37. Huang, Z., Gabriel, J. M., Baldwin, M. A., Fletterick, R. J., Prusiner. S. B. & Cohen, F. E. (1994) Proc. Natl. Acad. Sci. USA 91, 7139-7143.
38. Lansbury, P. T. (1994) Science 265. 1510.
39. Nguyen, J., Baldwin, M. A., Cohen, F. E. & Prusiner, S. B. (1995) Biochemistry 34, 4186-4192.
40. Riek, R., Hornemann, S., Wider, G., Billeter, M., Glocksbuber, R. & Wuthrich, K. (1996) Nature 382, 180-182.
41. Glockshuber, R., Hornemann, S., Riek, R., Wider, G., Billeter, M. & Wuthrich, K. (1997) Trends Biochem. Sci. 22, 241-242.
42. Harrison, P. M., Bamborough, P., Daggett, V., Prusiner, S. B. & Cohen. F. E. (1997) Curr. Opin. Struct. Biol. 7, 53-59.
43. Cohen, F. E. (1999) J. Mol. Biol. 293, 313-320.
44. Glover, K. J., Martini, P. M., Vold, R. R. & Komives, E. A. (1999) Anal. Biochem. 272, 270-274.
45. Cappai, R., Jobling, M. F., Barrow, C. J. & Collins, S. (2001) Contrib. Microbiol. 7, 32-47.
46. Derreumaux, P. (2001) Biophys. J. 81, 1657-1665.
47. Eberl, H. & Glockshuber, R. (2002) Biophys. Chem. 96, 293-303.
48. Linhananta, A., Zhou, H. & Zhou, Y. (2002) Protein Sci. 11, 1695-1701.
49. Macdonald, J. R. & Johnson, W. C., Jr. (2001) Protein Sci 10, 1172-1177.
50. Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225.
51. Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C. E. M. & Baker, D. (2001) Proteins 45, Suppl., 119-126.
52. Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker, D. (1999) Proteins Struct. Funct. Genet. 34, 82-95.
53. Meiler, J., Bradley, P., Misura, K., Wedemeyer, W., Schief, B. & Baker, D. (2003) Proteins Struct. Funct. Genet., in press.
54. Habohm, U., Scharf, M., Schneider, R. & Sander, C. (1992) Protein Sci. 1, 409-417.
55. Bujnicki, J. M., Elofsson, A., Fischer, D. & Rychlewski, L. (2001) Proteins Struct. Funct. Genet. 5, Suppl., 184-195.
56. Barrette-Ng, I. H., Ng, K. K., Mark, B. L., Van Aken, D., Cherney, M. M., Garen, C., Kolodenko, Y., Gorbalenya, A. E., Snijder, E. J. & James, M. N. (2002) J. Biol. Chem. 277, 39960-39966.
57. Lehmann, C., Lim, K, Chalamasetty, V. R., Krajewski, W., Melamud, E., Galkin, A., Howard, A., Kelman, Z., Reddy, P. T., Murzin, A. G. & Herzberg, O. (2003) Proteins 50, 249-260.
58. Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, T. & Yokoyama, S. (2002) Mol. Cell 10, 359-371.