Less is more: Towards an optimal universal description of protein folds

Bioinformatics

Volumn 21, Issue SUPPL. 2, 2005, Pages

  Szustakowski, Joseph D ^a   Kasif, Simon ^a,b   Weng, Zhiping ^a,b  

^a Boston University   (United States)

^b BOSTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BIOINFORMATICS; GENE CLUSTER; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REGULATORY MECHANISM; SEQUENCE ALIGNMENT; SIMULATION;

EID: 27544482366     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1111     Document Type: Article

References (42)

1. Born,C. and Kerbosch,J. (1973) Finding all cliques of an undirected graph. Commun. ACM, 16, 575-577.
2. Boutonnet,N.S. et al. (1998) Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins. Proteins, 30, 193-212.
3. Brenner,S.E. et al. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
4. Cormen,T.H. (2001) Introduction to Algorithms. MIT Press, Cambridge, MA,
5. Day,R. et al. (2003) A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci., 12, 2150-2160.
6. Dietmann,S. and Holm,L. (2001) Identification of homology in protein structure classification. Nat. Struct. Biol., 8, 953-957.
7. Dunbrack,R.L., Jr., Gerloff,D.L., Bower,M., Chen,X., Lichtarge,O. and Cohen,F.E. (1997) Meeting review: The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, California, December 13-16, 1996. Fold. Design, 2, R27-R42.
8. Efimov,A.V. (1984) A novel super-secondary structure of proteins and the relation between the structure and amino acid sequence. FEBS Lett., 166, 33-38.
9. Fredman,M. and Tarjan,R. (1987) Fibonacci heaps and their uses in improving network optimization algorithms. J. Assoc. Comput. Mach., 34, 596-615.
10. Frishman,D. and Argos,P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
11. Gerstein,M. and Levitt,M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci., 7, 445-456.
12. Grishin,N.V. (2001) Fold change in evolution of protein structures. J. Struct. Biol., 134, 167-185.
13. Harrison,A. et al. (2002) Quantifying the similarities within fold space. J. Mol. Biol., 323, 909-926.
14. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
15. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-603.
16. Jones,D.T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol., 7, 377-387.
17. Lindqvist,Y. and Schneider,G. (1997) Circular permutations of natural protein sequences: Structural evidence. Curr. Opin. Struct. Biol., 7, 422-427.
18. Lupas,A.N. et al. (2001) On the evolution of protein folds: Are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol., 134, 191-203.
19. Marchler-Bauer,A. and Bryant,S.H. (1997) A measure of success in fold recognition. Trends Biochem. Sci., 22, 236-240.
20. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
21. Orengo,C.A. et al. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
22. Orengo,C.A. et al. (1999) The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res., 27, 275-279.
23. Pearl,F.M. et al. (2000) Assigning genomic sequences to CATH. Nucleic Acids Res., 28, 277-282.
24. Presnell,S.R. and Cohen,F.E. (1989) Topological distribution of four-alpha-helix bundles. Proc. Natl Acad. Sci. USA, 86, 6592-6596.
25. Quinlan,J.R. and Rivest,R.L. (1989) Inferring decision trees using the minimum description length principle. Inform. Comput., 80, 227-248.
26. Richardson,J.S. (1977) β-Sheet topology and the relatedness of proteins. Nature, 268, 495-500.
27. Rissanen,J. (1978) Modeling by shortest data description. Automatic, 14, 37-38.
28. Rissanen,J. (1986) Stochastic complexity and modeling. Ann. Stat., 14, 1080-1100.
29. Rissanen,J. (1987) Stochastic complexity. J. R. Statist. Soc. Ser. B, 49, 223-239 and 253-265.
30. Salem,G.M. et al. (1999) Correlation of observed fold frequency with the occurrence of local structural motifs. J. Mol. Biol., 287, 969-981.
31. Shindyalov,I.N. and Bourne,P.E. (2000) An alternative view of protein fold space. Proteins, 38, 247-260.
32. Simons,K.T. et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
33. Simons,K.T. et al. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins (suppl.), 171-176.
34. Smith,T.F. et al. (1997) Current limitations to protein threading approaches. J. Comput. Biol., 4, 217-225.
35. Swindells,M.B. et al. (1998) Contemporary approaches to protein structure classification. Bioessays, 20, 884-891.
36. Szustakowski,J.D. and Weng,Z. (2000) Protein structure alignment using a genetic algorithm. Proteins, 38, 428-440.
37. Szustakowski,J.D. and Weng,Z. (2002) K2: Protein structure comparisons and their statistical significance. In Fogel,G. and Corne,D. (eds), Evolutionary Computation in Bioinformatics. Morgan Kaufmann.
38. Szustakowski,J.D. (2003) A protein structure alignment method and application to the discovery of recurrent protein structure motifs. Doctoral dissertation, Boston University, Boston, MA.
39. Taylor,W.R. (2002) A 'periodic table' for protein structures. Nature, 416, 657-660.
40. Wolf,Y.I. et al. (2000) Estimating the number of protein folds and families from complete genome data. J. Mol. Biol., 299, 897-905.
41. Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol., 301, 679-689.
42. Zhang,C. and DeLisi,C. (1998) Estimating the number of protein folds. J. Mol. Biol., 284, 1301-1305.