Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

Proteins: Structure, Function and Genetics

Volumn 58, Issue 1, 2005, Pages 166-179

  Chandonia, John Marc ^a   Brenner, Steven E ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEOME;

ANALYTIC METHOD; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; DATA BASE; ESCHERICHIA COLI; EUKARYOTE; GENE TARGETING; GENOMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURAL GENE; STRUCTURE ANALYSIS;

ANIMALS; DATABASES, PROTEIN; GENE TARGETING; GENOME; HUMANS; MULTIGENE FAMILY; PROTEINS; PROTEOMICS;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 10844244823     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20298     Document Type: Article

References (37)

1. Burley SK, Bonanno JB. Structural genomics. Methods Biochem Anal 2003;44:591-612.
2. Blundell TL, Mizuguchi K. Structural genomics: an overview. Prog Biophys Mol Biol 2000;73:289-295.
3. Brenner SE. A tour of structural genomics. Nat Rev Genet 2001;2:801-809.
4. Montelione GT. Structural genomics: an approach to the protein folding problem. Proc Natl Acad Sci USA 2001;98:13488-13489.
5. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci 2002;11:723-738.
6. Brenner SE, Berry A. A quantitative methodology for the de novo design of proteins. Protein Sci 1994;3:1871-1882.
7. Brenner SE. Target selection for structural genomics. Nat Struct Biol 2000;Suppl 7:967-969.
8. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
9. Whisstock JC, Lesk AM. Prediction of protein function from protein sequence and structure. Q Rev Biophys 2003;36:307-340.
10. Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001;307:1113-1143.
11. Goldsmith-Fischman S, Honig B. Structural genomics: computational methods for structure analysis. Protein Sci 2003;12:1813-1821.
12. PSI-phase 1 and beyond. Nat Struct Mol Biol 2004;11:201.
13. Harrison SC. Whither structural biology? Nat Struct Mol Biol 2004;11:12-15.
14. Matte A, Sivaraman J, Ekiel I, Gehring K, Jia Z, Cygler M. Contribution of structural genomics to understanding the biology of Escherichia coli. J Bacteriol 2003;185:3994-4002.
15. Goulding CW, Apostol M, Anderson DH, Gill HS, Smith CV, Kuo MR, Yang JK, Waldo GS, Suh SW, Chauhan R, Kale A, Bachhawat N, Mande SC, Johnston JM, Lott JS, Baker EN, Arcus VL, Leys D, McLean KJ, Munro AW, Berendzen J, Sharma V, Park MS, Eisenberg D, Sacchettini J, Alber T, Rupp B, Jacobs W Jr, Terwilliger TC. The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr Drug Targets Infect Disord 2002;2:121-141.
16. Liu J, Rost B. Target space for structural genomics revisited. Bioinformatics 2002;18:922-933.
17. Vitkup D, Melamud E, Moult J, Sander C. Completeness in structural genomics. Nat Struct Biol 2001;8:559-566.
18. Liu J, Hegyi H, Acton TB, Montelione GT, Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins 2004;56:188-200.
19. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database [Database issue]. Nucleic Acids Res 2004;32:D138-D141.
20. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31:365-370.
21. Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res 2003;31:414-417.
22. Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994;18:269-285.
23. Lupas A. Prediction and analysis of coiled-coil structures. Methods Enzymol 1996;266:513-525.
24. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-580.
25. Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003;31:38-42.
26. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. Hidden Markov models in computational biology: applications to protein modeling. J Mol Biol 1994;235:1501-1531.
27. Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14:755-763.
28. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle, E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003;31:315-318.
29. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
30. Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998;95:6073-6078.
31. Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004 [Database issue]. Nucleic Acids Res 2004;32:D189-D192.
32. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources [Database issue]. Nucleic Acids Res 2004;32:D217-D222.
33. Heger A, Holm L. More for less in structural genomics. J Struct Funct Genomics 2003;4:57-66.
34. Burley SK, Bonanno JB. Structural genomics of proteins from conserved biochemical pathways and processes. Curr Opin Struct Biol 2002;12:383-391.
35. Apic G, Gough J, Teichmann SA. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001;310:311-325.
36. Apic G, Huber W, Teichmann SA. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics 2003;4:67-78.
37. Lee D, Grant A, Buchan D, Orengo C. A structural perspective on genome evolution. Curr Opin Struct Biol 2003;13:359-369.