From fold recognition to homology modeling: An analysis of protein modeling challenges at different levels of prediction complexity

Computers and Chemistry

Volumn 24, Issue 3-4, 2000, Pages 499-510

  Olszewski, Krzysztof A ^a   Yan, Lisa ^a   Edwards, David ^a   Yeh, Tina ^a  

^a ACCELRYS INC   (United States)

Author keywords

CASP3; Fold recognition; Homology modeling

Indexed keywords

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PREDICTION AND FORECASTING; PROTEIN FOLDING; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PREDICTIVE VALUE OF TESTS; PROTEIN FOLDING; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0034184864     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(99)00078-9     Document Type: Article

References (41)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. J. Mol. Biol. 215, 403.
2. Altschul, S.F., Madden, T., Schaffer, A., et al., 1997. Nucleic Acid Res. 25, 3389.
3. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D., Sonnhammer, E.L.L., 1999. Nucleic Acids Res. 27, 260.
4. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.E Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M., 1977. J. Mol. Biol. 112, 535.
5. Bowie, J.V., Luethy, R., Eisenberg, D., 1991. Science 253, 164.
6. CASP3, 1998. http://PredictionCenter.llnl.gov/casp3/Casp3.html.
7. Di Francesco, V., Geetha, V., Garnier, J., Munson, P.J., 1997. Proteins Suppl 1, 123.
8. Eddy, S.R., 1996. Curr. Op. Struct. Biol. 6, 361.
9. Fischer, D., Eisenberg, D., 1997. Proc. Natl. Acad. Sci. USA 94, 11929.
10. Godzik, A., Skolnick, J., 1992. Proc. Natl. Acad. Sci. USA 89, 1209.
11. Gribskov, M., McLachlan, A.D., Eisenberg, D., 1987. Proc. Natl. Acad. Sci. USA 84, 4355.
12. Hargbo, J., Elofsson, A., 1999. Proteins Struct. Funct. Genet. 36, 68.
13. Holm, L., Sander, C., 1993. J. Mol. Biol. 233, 123.
14. Homology, 1998. User Manual, Molecular Simulations, San Diego.
15. Jones, D., Taylor, W.R., Thorton, J.M., 1992. Nature 358, 86.
16. Kabsch, W., Sander, C., 1983. Biopolymers 22, 2577.
17. Kelley, L.A., MacCallum, R.M., Sternberg, M., Karplus, K., Fischer, D., Elofsson, A., Godzik, A., Rychlewski, L., Pawłowski, K., Jones, D., Bryson, K., Rost, B., 1999. Proteins 00, 0000.
18. King, R.D., Sternberg, M.J.E., 1996. Protein Sci. 5, 2298.
19. Krogh, A., Brown, M., Mian, I.S., Sjolander, K., Haussler, D., 1994. J. Mol. Biol. 235, 1501.
20. Lichtarge, O., Bourne, U.R., Cohen, F.E., 1996. J. Mol. Biol. 257, 342.
21. Luethy, R., Bowie, J.U., Eisenberg, D., 1992. Nature 356, 83.
22. Murzin, A.G., 1999. Available from CASP3, 1998.
23. Murzin, A.G., Brenner, S.E., Hubbard, T., Chotia, C., 1995. J. Mol. Biol. 247, 536.
24. Olszewski, K.A., 1998. Pol. J. Chem. 72, 1667.
25. Olszewski K.A., 2000, Proc. Pac. Biocomput. Symp. 143.
26. Olszewski, K.A., Yan, L., Edwards, D.J., 1999. Theor. Chem. Acc. 111, 57.
27. Park, J., Teichmann, S.A., Hubbard, T., Chotia, C., 1997. J. Mol. Biol. 273, 349.
28. Pawłowski, K., Bierzyński, A., Godzik, A., 1996. J. Mol. Biol. 256, 349.
29. Pawłowski, K., Baohong, Z., Rychlewski, L., Godzik, A., 1999. Proteins Struct. Funct. Genet. 36, 20.
30. Pearson, W.R., 1988. Proc. Natl. Acad. Sci USA 85, 2444.
31. Rice, D., Eisenberg, D., 1997. J. Mol. Biol. 267, 1026.
32. Rost, B., Schneider, R., Sander, C., 1997. J. Mol. Biol. 270, 471.
33. Russel, R.B., Copley, R.R., Barton, G.J., 1996. J. Mol. Biol. 259, 349.
34. Rychlewski, L., Zhang, B., Godzik, A., 1998. Fold Des. 3, 229.
35. Šali, A., Blundell, T.L., 1993. J. Mol. Biol. 234, 779.
36. Sanchez, R., Šali, A., 1998. Proc. Natl. Acad. Sci. USA 95, 13597.
37. SeqFold, 1998. SeqFold release 1.0, Molecular Simulations.
38. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. Nucleic Acid Res. 22, 4676.
39. Venclovas, C., Fidelis, K.A., 1998. CAPS3 Presentation.
40. Yan, L., Zhu, Z.-Y., Badretdinov, A., Olszewski, K.A., Kitson, D., Pear, M., 2000. In preparation.
41. Yi, T.M., Lander, E.S., 1994. Protein Sci. 3, 1315.