Are predicted structures good enough to preserve functional sites?

Structure

Volumn 7, Issue 6, 1999, Pages 643-650

  Wei, Liping ^a   Huang, Enoch S ^b   Altman, Russ B ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Calcium binding site; Function analysis; Sidechain modeling; Site recognition; Structure prediction

Indexed keywords

CALCIUM BINDING PROTEIN;

ARTICLE; BINDING SITE; CALCIUM BINDING; CATTLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 1842830270     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80085-9     Document Type: Article

References (27)

1. References Eisenhaber, F., Persson, B. & Argos, P. (1995). Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol. 30, 1-94.
2. Moult, J., Hubbard, T., Bryant, S.H., Fidelis, K. & Pedersen, J.T. (1997). Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins (Supplement 1), 2-6.
3. Bairoch, A. & Apweiler, R. (1997). The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res. 25, 31-36.
4. Bernstein, F.C., et al., & Tasumi, M. (1977). The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
5. Moult, J., Pedersen, J.T., Judson, R. & Fidelis, K. (1995). A large-scale experiment to assess protein structure prediction methods. Proteins 23, ii-v.
6. Venclovas, C., Zemla, A., Fidelis, K. & Moult, J. (1997). Criteria for evaluating protein structures derived from comparative modeling. Proteins (Supplement 1), 7-13.
7. Martin, A.C., MacArthur, M.W. & Thornton, J.M. (1997). Assessment of comparative modeling in CASP2. Proteins (Supplement 1), 14-28.
8. Marchler-Bauer, A. & Bryant, S.H. (1997). Measures of threading specificity and accuracy. Proteins (Supplement 1), 74-82.
9. Marchler-Bauer, A., Levitt, M. & Bryant, S.H. (1997). A retrospective analysis of CASP2 threading predictions. Proteins (Supplement 1), 83-91.
10. Zemla, A., Venclovas, C., Reinhardt, A., Fidelis, K. & Hubbard, T.J. (1997). Numerical criteria for the evaluation of ab initio predictions of protein structure. Proteins (Supplement 1), 140-150.
11. Lesk, A.M. (1997). CASP2: Report on ab initio predictions. Proteins (Supplement 1), 151-166.
12. Fetrow, J.S., Godzik, A. & Skolnick, J. (1998). Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282, 703-711.
13. Fetrow, J.S. & Skolnick, J. (1998). Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281, 949-968.
14. McPhalen, C.A., Strynadka, N.C. & James, M.N. (1991). Calcium-binding sites in proteins: A structural perspective. Adv. Protein Chem. 42, 77-144.
15. 2+ binding sites in proteins. Proc. Natl Acad Sci. USA 91, 817-821.
16. Yamashita, M.M., Wesson, L., Eisenman, G. & Eisenberg, D. (1990). Where metal ions bind in proteins. Proc. Natl Acad. Sci. USA 87, 5648-5652.
17. Wei, L. & Altman, R.B. (1998). In Pacific Symposium on Biocomputing. (Altman, R.B., Dunker, A.K., Hunter, L. & Klein, T.E., eds), pp. 497-508, World Scientific, Maui, Hawaii.
18. Szebenyi, D.M. & Moffat, K. (1986). The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium- Binding proteins. J. Biol. Chem. 261, 8761-8777.
19. Szebenyi, D.M., Obendorf, S.K. & Moffat, K. (1981). Structure of vitamin D-dependent calcium-binding protein from bovine intestine. Nature 294, 327-332.
20. Park, B. & Levitt, M. (1996). Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258, 367-392.
21. Park, B.H., Huang, E.S. & Levitt, M. (1997). Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266, 831-846.
22. Wei, L., Chang, J.T. & Altman, R.B. (1998). Statistical analysis of protein structures: Using environmental features for multiple purposes. In Computational Methods in Molecular Biology. (Salzberg, S., Searls, D. & Kasif, S., eds), pp. 207-226, Elsevier Science, France.
23. Bagley, S.C. & Altman, R.B. (1996). Conserved features in the active site of nonhomologous serine proteases. Fold. Des. 1, 371-379.
24. Levitt, M. (1992). Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507-533.
25. Levitt, M., Hirshberg, M., Sharon, R. & Daggett, V. (1995). Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp. Phys. Commun. 91, 215-231.
26. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. (1988). The MIDAS display system. J. Mol. Graph. 6, 13-27.
27. Huang, C.C., Pettersen, E.F., Klein, T.E., Ferrin, T.E. & Langridge, R. (1991). Conic: A fast renderer for space-filling molecules with shadows. J. Mol. Graph. 9, 230-236.