Have we seen all structures corresponding to short protein fragments in the protein data bank? An update

Protein Engineering

Volumn 16, Issue 6, 2003, Pages 407-414

  Du, Peicheng ^a   Andrec, Michael ^a   Levy, Ronald M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Database; Fold; Loop modeling; Protein fragment; Protein structure

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; FACTUAL DATABASE; GENETICS; HUMAN; MOLECULAR MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0043268757     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzg052     Document Type: Article

References (32)

1. Andrec, M., Du, P. and Levy, R.M. (2001) J. Biomol. NMR, 21, 335-347.
2. Andrec, M., Harano Y., Jacobson, M.P., Friesner, R.A. and Levy, R.M. (2002) J. Stuct. Funct. Genomics, 2, 103-111.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res., 28, 235-242.
4. Brenner, S.E., Koehl, P. and Levitt, M. (2000) Nucleic Acids Res. 28, 254-256.
5. Bystroff, C. and Baker, D. (1998) J. Mol. Biol., 281, 565-577.
6. Chandonia, J.M., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M. and Brenner, S.E. (2002) Nucleic Acids Res., 30, 260-263.
7. Chothia, C. (1973) J. Mol. Biol., 75, 295-302.
8. Cornilescu, G., Delaglio, F. and Bax, A., (1999) J. Biomol. NMR, 13, 289-302.
9. Correa, P.E. (1990) Proteins, 7, 366-377.
10. Deane, C.M. and Blundell, T.L. (2000) Proteins, 40, 135-144.
11. Delaglio, F., Kontaxis, G. and Bax, A., (2000) J. Am. Chem. Soc., 122, 2142-2143.
12. Fidelis, K., Stern, P.S., Bacon, D. and Moult, J. (1994) Protein Eng., 7, 953-960.
13. Fiser, A., Feig, M., Brooks, C.L., III and Sali, A. (2002) Acc. Chem. Res., 35, 413-421.
14. Greer, J. (1980) Proc. Natl Acad. Sci. USA, 77, 3393-3397.
15. Holm, L. and Sander, C. (1991) J. Mol. Biol., 218, 183-194.
16. Jacobson, M.P., Friesner, R.A., Xiang, Z. and Honig, B., (2002a) J. Mol. Biol., 320, 597-608.
17. Jacobson, M.P., Kaminski, G.A., Friesner, R.A. and Rapp, C.S., (2002b) J. Phys. Chem. B, 106, 11673-11680.
18. Jones, T.A. and Thirup, S. (1986) EMBO J., 5, 819-822.
19. Kabsch, W. (1976) Acta Crystallogr., A32, 922-923.
20. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
21. Kolodny, R., Koehl, P., Guibas, L. and Levitt, M. (2002) J. Mol. Biol., 323, 297-307.
22. Kwasigroch, J., Chromilier, J. and Mornon J. (1996) J. Mol. Biol., 259, 855-872.
23. Lessel, U. and Schomburg, D. (1997) Protein Eng., 10, 659-664.
24. Levitt, M. (1992) J. Mol. Biol., 226, 507-533.
25. McLachlan, A.D. (1979) J. Mol. Biol., 128, 49-79.
26. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995). J. Mol. Biol., 247, 536-540.
27. Reid, L.S. and Thornton, J.M. (1989) Proteins, 5, 170-182.
28. Simons, K.T., Bonneau, R., Ruczinski, I. and Baker, D. (1999) Proteins, Suppl. 3, 171-176.
29. Sippl, M.J., Lackner, P., Domingues, F.S., Prlic, A., Malik, R., Andreeva, A. and Wiederstein, M. (2001) Proteins, Suppl. 5, 55-67.
30. Summers, N.L. and Karplus, M. (1990) J. Mol. Biol., 216, 991-1016.
31. van Vlijmen, H.W.T. and Karplus, M. (1997) J. Mol. Biol., 267, 975-1001.
32. Wojcik, J., Mornon, J. and Chomilier, J. (1999) J. Mol. Biol., 289, 1469-1490.