Prediction of protein domain boundaries from sequence alone

Protein Science

Volumn 12, Issue 4, 2003, Pages 696-701

  Galzitskaya, Oxana V ^a   Melnik, Bogdan S ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Degrees of freedom; Domain database; Latent entropy profile; Protein domain; Superfamily

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; DATA BASE; ENERGY TRANSFER; ENTROPY; HYPOTHESIS; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENTROPY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 0037377548     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0233103     Document Type: Article

References (19)

1. Adams, R.M., Das, S., and Smith, T.F. 1996. Multiple domain protein diagnostic patterns. Protein Sci. 5: 1240-1249.
2. Berezovsky, I.N., Namiot, V.A., Tumanyan, V.G., and Esipova, N.G. 1999. Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition. J. Biomol. Struct. Dyn. 17: 133-155.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The Protein Data Bank. A computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535-542.
4. Busetta, B. and Barrans, Y. 1984. The prediction of protein domains. Biochim. Biophys. Acta 790: 117-124.
5. Galzitskaya, O.V., Surin, A.K., and Nakamura, H. 2000. Optimal region of average side-chain entropy for fast protein folding. Protein Sci. 9: 580-586.
6. George, R.A. and Heringa, J. 1992. SnapDRAGON: A method to delineate protein structural domains from sequence data. J. Mol. Biol. 316: 839-851.
7. Gouzy, J., Corpet, F., and Kahn, D. 1999. Whole genome protein domain analysis using a new method for domain clustering. Comput. Chem. 23: 333-340.
8. Gracy, J. and Argos, P. 1998. Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities. Bioinformatics 14: 174-187.
9. Guan, X. and Du, L. 1998. Domain identification by clustering sequence alignments. Bioinformatics 14: 783-788.
10. Islam, S.A., Luo, J., and Sternberg, M.J. 1995. Identification and analysis of domains in proteins. Protein Eng. 8: 513-525.
11. Jones, S., Stewart, M., Michie, A., Swindells, M.B., Orengo, C., and Thornton, J.M. 1998. Domain assignment for protein structures using a consensus approach: Characterization and analysis. Protein Sci. 7: 233-242.
12. Kikuchi, T., Némethy, G., and Scheraga, H.A. 1988. Prediction of the location of structural domains in globular proteins. J. Protein Chem. 7: 427-471.
13. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
14. Park, J. and Teichmann, S.A. 1998. DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics 14: 144-150.
15. Richardson, J.S. 1981. The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34: 167-339.
16. Siddiqui, Q.S. and Barton, G.J. 1995. Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions. Protein Sci. 4: 872-884.
17. Sonnhammer, E.L.L. and Kahn, D. 1994. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3: 482-492.
18. Wetlaufer, D.B. 1973. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc. Natl Acad. Sci. 70: 697-701.
19. Wheelan, S.J., Marchler-Bauer, A., and Bryant, S.H. 2000. Domain size distributions can predict domain boundaries. Bioinformatics 16: 613-618.