How old is your fold?

Bioinformatics

Volumn 21, Issue SUPPL. 1, 2005, Pages

  Winstanley, Henry F ^a   Abeln, Sanne ^a   Deane, Charlotte M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; CONVERGENT EVOLUTION; CORRELATION ANALYSIS; GENE ASSIGNMENT; METHODOLOGY; MOLECULAR PHYLOGENY; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

AGE ESTIMATION; DATA TYPE; HIERARCHICAL METHOD; OCCURRENCE PATTERN; PROTEIN FOLDS; PROTEIN STRUCTURES;

ESTIMATION; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; PROTEIN FOLDING; TREES (MATHEMATICS);

PROTEINS;

EID: 29144471907     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1008     Document Type: Article

References (27)

1. Abeln,S. and Deane,C.M. (2005) Fold usage on genomes and protein fold evolution. Proteins, in press.
2. Altschul,S., Madden,T., Schäffer,A., Zhang,J., Zhang,Z., Miller,W., and Lipman,D. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Barabási,A. and Oltvai,Z. (2004) Network biology: Understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
4. Berman,H., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T., Weissig,H., Shindyalov,I. and Bourne,P. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
5. Caetano-Anollés,G. and Caetano-Anollés,D. (2003) An evolutionarily structured universe of protein architecture. Genome Res., 13, 1563-1571.
6. Cherkasov,A. and Jones,S. (2004) Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics, 5, 37.
7. Chothia,C. (1992) Proteins. One thousand families for the molecular biologist. Nature, 357, 543-544.
8. Coulson,A. and Moult,J. (2002) A unifold, mesofold, and superfold model of protein fold use. Proteins, 46, 61-71.
9. Eisenberg,E. and Levanon,E. (2003) Preferential attachment in the protein network evolution. Phys. Rev. Lett., 91, 138701.
10. Felsenstein,J. (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
11. Gough,J. and Chothia,C. (2002) SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res., 30, 268-272.
12. Harrison,A., Pearl,F., Mott,R., Thornton,J. and Orengo,C. (2002) Quantifying the similarities within fold space. J. Mol. Biol., 323, 909-926.
13. Hegyi,H., Lin,J., Greenbaum,D. and Gerstein,M. (2002) Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds. Proteins, 47, 126-141.
14. Karev,G., Wolf,Y., Rzhetsky,A., Berezovskaya,F. and Koonin,E. (2002) Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol. Biol., 2, 18.
15. Koonin,E.,Wolf,Y. and Karev,G. (2002) The structure of the protein universe and genome evolution. Nature, 420, 218-223.
16. Lin,J. and Gerstein,M. (2000) Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels. Genome Res., 10, 808-818.
17. Liu,X., Fan,K. and Wang,W. (2004) The number of protein folds and their distribution over families in nature. Proteins, 54, 491-499.
18. Mirkin,B., Fenner,T., Galperin,M. andKoonin,E. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3, 2.
19. Murzin,A. (1998) Howfar divergent evolution goes in proteins. Curr. Opin. Struct. Biol., 8, 380-387.
20. Murzin,A., Brenner,S., 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.
21. Qian,J., Luscombe,N. and Gerstein,M. (2001) Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model. J. Mol. Biol., 313, 673-681.
22. Ranea,J., Buchan,D., Thornton,J. and Orengo,C. (2004) Evolution of protein superfamilies and bacterial genome size. J. Mol. Biol., 336, 871-887.
23. Snel,B., Bork,P. and Huynen,M. (2002) Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res., 12, 17-25.
24. Taylor,W., Heringa,J., Baud,F. and Flores,T. (2002) A Fourier analysis of symmetry in protein structure. Protein Eng., 15, 79-89.
25. Wolf,Y., Brenner,S., Bash,P. and Koonin,E. (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res., 9, 17-26.
26. Xenarios,I., Salwínski,L., Duan,X., Higney,P., Kim,S. and Eisenberg,D. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
27. Yang,S., Doolittle,R. and Bourne,P. (2005) Phylogeny determined by protein domain content. Proc. Natl Acad. Sci. USA, 102, 373-378.