Exhaustive enumeration of protein domain families

Journal of Molecular Biology

Volumn 328, Issue 3, 2003, Pages 749-767

  Heger, Andreas ^a,b   Holm, Liisa ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Domain; Evolution; Homology; Maximum likelihood; Protein family

Indexed keywords

HOMEODOMAIN PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DATA BASE; DECOMPOSITION; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE HOMOLOGY; VALIDATION PROCESS;

EID: 0037414465     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00269-9     Document Type: Article

References (45)

1. Wetlaufer D.B. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc. Natl Acad. Sci. USA. 70:1973;697-701.
2. Doolittle R.F., Bork P. Evolutionarily mobile modules in proteins. Sci. Am. 269:1993;50-56.
3. Gribskov M., McLachlan A.D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA. 84:1987;4355-4358.
4. Eddy S. Profile hidden markov models. Bioinformatics. 14:1998;755-763.
5. Brazma A., Jonassen I., Eidhammer I., Gilbert D. Approaches to the automatic discovery of patterns in biosequences. J. Comput. Biol. 5:1998;279-305.
6. Vitkup D., Melamud E., Moult J., Sander C. Completeness in structural genomics. Nature Struct. Biol. 8:2001;559-566.
7. Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933.
8. Grundy W.N. Homology detection via family pairwise search. J. Comput. Biol. 5:1998;479-491.
9. Yona G., Linial N., Tishby N., Linial M. A map of the protein space - an automatic hierarchical classification of all protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6:1998;212-221.
10. Heger A., Holm L. Towards a covering set of protein family profiles. Prog. Biophys. Mol. Biol. 73:2000;321-337.
11. Krause A., Vingron M. A set-theoretic approach to database searching and clustering. Bioinformatics. 14:1998;430-438.
12. Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucl. Acids Res. 30:2002;1575-1584.
13. Corpet F., Gouzy J., Kahn D. Recent improvements of the prodom database of protein domain families. Nucl. Acids Res. 27:1999;263-267.
14. Gracy J., Argos P. Automated protein sequence database classification. ii. delineation of domain boundaries from sequence similarities. Bioinformatics. 14:1998;174-187.
15. Gould S., Eldregde N. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology. 3:1977;115-151.
16. Park J., Holm L., Heger A., Chothia C. Rsdb: representative protein sequence databases have high information content. Bioinformatics. 16:2000;458-464.
17. Heger A., Holm L. Rapid automatic detection and alignment of repeats in protein sequences. Proteins, Struct. Funct. Genet. 41:2000;224-237.
18. Wuchty S. Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18:2001;1694-1702.
19. Koonin E.V., Wolf Y.I., Karev G.P. The structure of the protein universe and genome evolution. Nature. 420:2002;218-223.
20. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., et al. The pfam protein families database. Nucl. Acids Res. 30:2002;276-280.
21. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., et al. Recent improvements to the smart domain-based sequence annotation resource. Nucl. Acids Res. 30:2002;242-244.
22. Doerks T., Copley R.R., Schultz J., Ponting C.P., Bork P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res. 12:2002;47-56.
23. Coutinho P., Henrissat B. Carbohydrate-active enzymes: an integrated database approach. Gilbert H., Davies G., Henrissat B., Svensson B. Recent Advances in Carbohydrate Bioengineering. 1999;3-12 The Royal Society of Chemistry, Cambridge, UK.
24. Heger A., Lappe M., Holm L. Accurate detection of very sparse sequence motifs. Proc. Annu. Int. Conf. Res. Comput. Mol. Biol. 2003;. In press.
25. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
26. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
27. Heger A., Holm L. Picasso: generating a covering set of protein family profiles. Bioinformatics. 17:2001;272-279.
28. Bairoch A., Apweiler R. The swiss-prot protein sequence database and its supplement trembl in 2000. Nucl. Acids Res. 28:2000;45-48.
29. Wu C.H., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z.Z., et al. The protein information resource: an integrated public resource of functional annotation of proteins. Nucl. Acids Res. 30:2002;35-37.
30. Westbrook J., Feng Z., Jain S., Bhat T.N., Thanki N., Ravichandran V., et al. The protein data bank: unifying the archive. Nucl. Acids Res. 30:2002;245-248.
31. Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., et al. The ensembl genome database project. Nucl. Acids Res. 30:2002;38-41.
32. Gish, W., (1997). nrdb - quasi-non-redundant database generator.
33. Holm L., Sander C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics. 14:1998;423-429.
34. Li W., Jaroszewski L., Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 17:2001;282-283.
35. Promponas V.J., Enright A.J., Tsoka S., Kreil D.P., Leroy C., Hamodrakas S., et al. Cast: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics. 16:2000;915-922.
36. Sonnhammer E.L., von Heijne G., Krogh A. A hidden markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6:1998;175-182.
37. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science. 252:1991;1162-1164.
38. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped blast and psi-blast: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
39. Kruskal J. On the shortest spanning subtree of a graph and the travelling salesman problem. Proc. Am. Math. Soc. 7:1956;48-50.
40. Sjolander K., Karplus K., Brown M., Hughey R., Krogh A., Mian I.S., Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12:1996;327-345.
41. Smith T., Waterman M. Indentification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
42. Brenner S.E., Chothia C., Hubbard T.J. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA. 95:1998;6073-6078.
43. Park J., Karplus K., Barrett C., Hughey R., Haussler D., Hubbard T., Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284:1998;1201-1210.
44. Soisson S.M., MacDougall-Shackleton B., Schleif R., Wolberger C. The 1.6 Å crystal structure of the arac sugar-binding and dimerization domain complexed with D-fucose. J. Mol. Biol. 273:1997;226-237.
45. Kraulis P. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.