Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds

BMC Structural Biology

Volumn 6, Issue , 2006, Pages

  Sadreyev, Ruslan I ^a   Grishin, Nick V ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE MAPPING; GENOME; MOLECULAR DYNAMICS; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TAXONOMY;

DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; GENOMICS; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33646487174     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-6     Document Type: Article

References (45)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235-242.
2. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005:D154-159.
3. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2005:D34-38.
4. Burley SK: An overview of structural genomics. Nat Struct Biol 2000, 7(Suppl):932-934.
5. Todd AE, Marsden RL, Thornton JM, Orengo CA: Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 2005, 348(5):1235-1260.
6. Abagyan RA, Batalov S: Do aligned sequences share the same fold? J Mol Biol 1997, 273(1):355-368.
7. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 2004:D226-229.
8. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30(1):276-280.
9. Holm L, Sander C: The FSSP database of structurally aligned protein fold families. Nucleic Acids Res 1994, 22(17):3600-3609.
10. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P: SMART 4.0: towards genomic data integration. Nucleic Acids Res 2004:D142-144.
11. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, et al.: InterPro, progress and status in 2005. Nucleic Acids Res 2005:D201-205.
12. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
13. Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM: The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics 2002, 2(1):11-21.
14. Grishin NV: Fold change in evolution of protein structures. J Struct Biol 2001, 134(2-3):167-185.
15. Alexandrov NN, Go N: Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Protein Sci 1994, 3(6):866-875.
16. Blundell TL, Johnson MS: Catching a common fold. Protein Sci 1993, 2(6):877-883.
17. Brenner SE, Chothia C, Hubbard TJ: Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 1997, 7(3):369-376.
18. Chothia C: Proteins. One thousand families for the molecular biologist. Nature 1992, 357(6379):543-544.
19. Coulson AF, Moult J: A unifold, mesofold, and superfold model of protein fold use. Proteins 2002, 46(1):61-71.
20. Govindarajan S, Recabarren R, Goldstein RA: Estimating the total number of protein folds. Proteins 1999, 35(4):408-414.
21. Holm L, Sander C: Mapping the protein universe. Science 1996, 273(5275):595-603.
22. Orengo CA, Jones DT, Thornton JM: Protein superfamilies and domain superfolds. Nature 1994, 372(6507):631-634.
23. Wang ZX: How many fold types of protein are there in nature? Proteins 1996, 26(2):186-191.
24. Wang ZX: A re-estimation for the total numbers of protein folds and superfamilies. Protein Eng 1998, 11(8):621-626.
25. Wolf YI, Grishin NV, Koonin EV: Estimating the number of protein folds and families from complete genome data. J Mol Biol 2000, 299(4):897-905.
26. Zhang C, DeLisi C: Estimating the number of protein folds. J Mol Biol 1998, 284(5):1301-1305.
27. Zhang CT: Relations of the numbers of protein sequences, families and folds. Protein Eng 1997, 10(7):757-761.
28. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al.: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
29. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278(5338):631-637.
30. Heger A, Holm L: Exhaustive enumeration of protein domain families. J Mol Biol 2003, 328(3):749-767.
31. Heger A, Wilton CA, Sivakumar A, Holm L: ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res 2005:D188-191.
32. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
33. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29(14):2994-3005.
34. Brenner SE, Koehl P, Levitt M: The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000, 28(1):254-256.
35. Chandonia JM, Hon G, Walker NS, L Conte L, Koehl P, Levitt M, Brenner SE: The ASTRAL Compendium in 2004. Nucleic Acids Res 2004:D189-192.
36. Caetano-Anolles G, Caetano-Anolles D: An evolutionarily structured universe of protein architecture. Genome Res 2003, 13(7):1563-1571.
37. Wolf YI, Brenner SE, Bash PA, Koonin EV: Distribution of protein folds in the three superkingdoms of life. Genome Res 1999, 9(1):17-26.
38. Cort JR, Yee A, Edwards AM, Arrowsmith CH, Kennedy MA: Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum. J Mol Biol 2000, 302(1):189-203.
39. Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA: XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. Genes Dev 2003, 17(8):977-990.
40. Yamasaki M, Moriwaki S, Miyake O, Hashimoto W, Murata K, Mikami B: Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold. J Biol Chem 2004, 279(30):31863-31872.
41. Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S: Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8. J Struct Funct Genomics 2005, 6(1):21-32.
42. Li W, Jaroszewski L, Godzik A: Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002, 18(1):77-82.
43. Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN: Toward consistent assignment of structural domains in proteins. J Mol Biol 2004, 339(3):647-678.
44. Structural Genomics Target Query [http://pdbbeta.rcsb.org/pdb/search/ getSgTargets.do]
45. Krishna SS, Sadreger RI, Grishin NV: A tale of two ferredoxins: sequence similarity and structural differences. BMC Struct Biol 2006, 6:8.