Fold assignments for amino acid sequences of the CASP2 experiment

Proteins: Structure, Function and Genetics

Volumn 29, Issue SUPPL. 1, 1997, Pages 113-122

  Rice, Danny W ^a   Fischer, Daniel ^a   Weiss, Robert ^a   Eisenberg, David ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Critical assessment of protein structure prediction; Protein fold assignment; Structure prediction

Indexed keywords

FERROCHELATASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; CHEMISTRY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; FERROCHELATASE; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 0031307341     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(1997)1+<113::aid-prot15>3.0.co;2-r     Document Type: Article

References (20)

1. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
2. Bowie, J.U., Luthy, R., Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170, 1991.
3. Zhang, Y.J.K., Eisenberg, D. The three-dimensional profile method using residue preference as a continuous function of residue environment. Protein Sci. 3:687-695, 1994.
4. Rice, D., Eisenberg, D. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol. 267:1026-1038, 1997.
5. Smith, T.F., Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197, 1981.
6. Needleman, S.B., Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453, 1970.
7. Fischer, D., Eisenberg, D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:947-955, 1996.
8. Fischer, D., Elofsson, A., Rice, D.W., Eisenberg, D. Assessing the performance of inverted protein folding methods by means of an extensive benchmark. Proceedings of the First Pacific Symposium on Biocomputing, Jan. 1996, pp. 300-318, http://www.mbi.ucla.edu/people/fischer/BENCH/benchmark1.html
9. Rost, B., Sander, C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232:584-599, 1993.
10. Rost, B. TOPITS: Threading one-dimensional predictions into three-dimensional structures. "Proceedings of the Conference on Intelligent Systems in Molecular Biology," ISMB-95, 1995:314-321.
11. Gonnet, G.H., Cohen, M.A., Benner, S.A. Exhaustive matching of the entire protein sequence database. Science 256: 1433-1445, 1992.
12. Elofsson, A., Fischer, D., Rice, D.W., Le Grand, S., Eisenberg, D. A study of combined structure-sequence profiles. Folding Design 1:451-461, 1996.
13. Russell, R.B., Copley, R.R., Barton, G.J. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259:349-365, 1996.
14. Frishman, D., Argos, P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 27:329-335, 1997.
15. Kabsh, C., Sander, W. Dictionary of protein structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
16. Gibrat, J-F., Madej, T., Bryant, S.H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6:377-385, 1996.
17. Al-Karadaghi, S., Hansson, M., Nikonov, S., Jonsson, B., Hederstedt, L. Crystal structure of ferrochelatase-The terminal enzyme in heme biosynthesis. Structure (in press), 1997.
18. Friedman, A.M., Fischmann, T.O., Steitz, T.A. Crystal structure of lac repressor core tetramer and its implications for dna looping. Science 268:1721-1727, 1995.
19. Kraulis, P.J. J. Appl. Crystallogr. 24:946-950, 1991.
20. Merritt, E.A., Murphy, M. Raster3D Version 2.0, a program for photorealistic molecular graphics. Acta Crystallogr. D50:869-873, 1994.