Constructing side chains on near-native main chains for ab initio protein structure prediction

Protein Engineering

Volumn 13, Issue 7, 2000, Pages 453-457

  Samudrala, Ram ^a   Huang, Enoch S ^b   Koehl, Patrice ^a   Levitt, Michael ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Cereon Genomics   (United States)

Author keywords

Conditional probability; Discriminatory function; Knowledge based; Protein structure prediction; Side chain construction

Indexed keywords

AMINO ACID;

ACCURACY; ARTICLE; COMPARATIVE STUDY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SIMULATION;

EID: 0033861004     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/13.7.453     Document Type: Article

References (35)

1. Bower, M., Cohen, F. and Dunbrack, R. (1997) J. Mol. Biol., 267, 1268-1282.
2. Diesenhofer, J. (1981) Biochemistry, 20, 2361-2370.
3. Dunbrack, R. (1999) Proteins: Struct. Funct. Genet., S3, 81-87.
4. Huang, E., Koehl, P., Levitt, M., Pappu, R. and Ponder, J. (1998a) J. Mol. Biol., 33, 204-217.
5. Huang, E., Samudrala, R. and Ponder, J. (1998b) Protein Sci., 7, 1998-2003.
6. Hubbard, T., Murzin, A., Brenner, S. and Chothia, C. (1997) Nucleic Acids Res., 25, 236-239.
7. Kissinger, C.R., Liu, B.S., Martin-Blanco, E. Kornberg, T.B. and Pablo, C.O. (1990) Cell, 63, 579-590.
8. Koehl, P. and Delarue, M. (1994) J. Mol. Biol., 239, 249-275.
9. Koehl, P. and Levitt, M. (1999) Nature Struct. Biol., 6, 108-111.
10. Lee, J., Liwo, A., Ripoll, D., Pillardy, J. and Scheraga, J. (1999) Proteins: Struct. Funct. Genet., S3, 204-208.
11. Levitt, M. (1974) J. Mol. Biol., 82, 393-420.
12. Levitt, M. (1983) J. Mol. Biol., 168, 595-620.
13. Levitt, M. (1992) J. Mol. Biol., 226, 507-533.
14. Levitt, M. and Lifson, S. (1969) J. Mol. Biol., 46, 269-279.
15. Levitt, M., Hirshberg, M., Sharon, R. and Daggett, V. (1995) Comput. Phys. Commun., 91, 215-231.
16. McLachlan, A. (1979) J. Mol. Biol., 128, 49-79.
17. Mondragon, A., Subbiah, S., Almo, S.C., Drottar, M. and Harrison, S.C. (1989) J. Mol. Biol., 205, 189-200.
18. Moult, J., Hubbard, T., Fidelis, K. and Pedersen, J. (1999) Proteins: Struct. Funct. Genet., S3, 2-6.
19. Mumenthaler, C. and Braun, W. (1995) Protein Eng., 4, 863-871.
20. Orengo, C., Bray, J., Hubbard, T., LoConte, L. and Sillitoe, J. (1999) Proteins: Struct. Funct. Genet., S3, 149-170.
21. Ortiz, A., Kolinkski, A., Rotkiewicz, P., Ilkowski, B. and Skolnick, J. (1999) Proteins: Struct. Funct. Genet., S3, 177-185.
22. Osguthorpe, D. (1999) Proteins: Struct. Funct. Genet., S3, 186-193.
23. Park, B., Huang, E. and Levitt, M. (1997) J. Mol. Biol., 266, 831-846.
24. Park, B. and Levitt, M. (1995) J. Mol. Biol., 249, 493-507.
25. Park, B. and Levitt, M. (1996) J. Mol. Biol., 258, 367-392.
26. Pedersen, J.T. and Moult, J. (1997) J. Mol. Biol., 269, 240-259.
27. Samudrala, R. and Moult, J. (1998a) J. Mol. Biol., 275, 895-916.
28. Samudrala, R. and Moult, J. (1998b) Protein Eng., 11, 991-997.
29. Samudrala, R., Xia, Y., Huang, E. and Levitt, M. (1999) Proteins: Struct. Funct. Genet., S3, 194-198.
30. Satow, Y., Cohen, G., Padlan, E. and Davies, D. (1986) J. Mol. Biol., 190, 593-604.
31. Simons, K., Kooperberg, C., Huang, E. and Baker, D. (1997) J. Mol. Biol., 268, 209-225.
32. Simons, K., Bonneau, R., Ruczinski, I. and Baker, D. (1999) Proteins: Struct. Funct. Genet., S3, 171-176.
33. Sun, S. (1993) Protein Sci., 2, 762-785.
34. Vijay-Kumar, S., Bugg, C.E. and Cook, W.J. (1987) J. Mol. Biol., 194, 531-544.
35. Xia, Y., Huang, E.S., Levitt, M. and Samudrala, R. (2000) J. Mol. Biol., 300, 171-185.