Pfam 10 years on: 10 000 families and still growing

Briefings in Bioinformatics

Volumn 9, Issue 3, 2008, Pages 210-219

  Sammut, Stephen John ^a   Finn, Robert D ^c   Bateman, Alex ^b  

^a UNIVERSITY OF MALTA   (Malta)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c NONE

Author keywords

Classification; Coverage; Hidden Markov model; Pfam; Protein families

Indexed keywords

ABELSON KINASE; ABELSON KINASE I;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; MOLECULAR EVOLUTION; PFAM DATABASE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS;

DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 43149094164     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn010     Document Type: Article

References (34)

1. Eisenberg D, Marcotte EM, Xenarios I, et al. Protein function in the post-genomic era. Nature 2000;405:823-6.
2. Finn RD, Mistry J, Schuster-Bockler B, et al. Pfam: Clans, web tools and services. Nucleic Acids Res 2006;34: D247-51.
3. Sonnhammer ELL, Eddy SR, Durbin R. Pfam: A comprehensive database of protein domain families based on seed alignments. Proteins 1997; 28:405-20.
4. Chothia C. Proteins. One thousand families for the molecular biologist. Nature 1992;357:543-4.
5. The UniProt Consortium. The Universal Protein Resource (UniProt). Nucleic Acids Res 2007;35:D193-7.
6. Bru C, Courcelle E, Carrere S, et al. The ProDom database of protein domain families: More emphasis on 3D. Nucleic Acids Res 2005;33:D212-5.
7. Stahelin RV, Long F, Peter BJ, et al. Contrasting membrane interaction mechanisms of AP180 N-terminal homology (ANTH) and epsin N-terminal homology (ENTH) domains. J Biol Chem 2003;278 28993-9.
8. Murzin AG, Brenner SE, Hubbard T, et al. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247:536-40.
9. Pearl FM, Bennett CF, Bray JE, et al. The CATH database: An extended protein family resource for structural and functional genomics. Nucleic Acids Res 2003;31:452-5.
10. Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000;28:235-42.
11. Kunin V, Cases I, Enright AJ, et al. Myriads of protein families, and still counting. Genome Biol 2003;4:401.
12. Orengo CA, Thornton JM. Protein families and their evolution - a structural perspective. Annu Rev Biochem 2005; 74:867-900.
13. Lee D, Grant A, Buchan D, et al. A structural perspective on genome evolution. Curr Opin Struct Biol 2003;13:359-69.
14. Liu J, Rost B. CHOP proteins into structural domain-like fragments. Proteins 2004;55:678-88.
15. Heger A, Holm L. Exhaustive enumeration of protein domain families. J Mol Biol 2003;328:749-67.
16. Enright AJ, Ouzounis CA. GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics 2000;16 451-7.
17. Lee D, Grant A, Marsden RL, et al. Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins 2005;59:603-15.
18. Heger A, Wilton CA, Sivakumar A, et al. ADDA: A domain database with global coverage of the protein universe. Nucleic Acids Res 2005;33:D188-91.
19. Veloso F, Riadi G, Aliaga D, et al. Large-scale, multigenome analysis of alternate open reading frames in bacteria and archaea. OMICS 2005;9:91-105.
20. Rost B. Did evolution leap to create the protein universe? Curr Opin Struct Biol 2002;12:409-16.
21. Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 2003;53:241-51.
22. Siew N, Fischer D. Structural biology sheds light on the puzzle of genomic ORFans. J Mol Biol 2004;342:369-73.
23. Daubin V, Ochman H. Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res 2004;14:1036-42.
24. Fischer D, Eisenberg D. Finding families for genomic ORFans. Bioinformatics 1999;15:759-62.
25. Gokhale RS, Khosla C. Role of linkers in communication between protein modules. Curr Opin Chem Biol 2000; 4:22-7.
26. Robinson CR, Sauer RT. Optimizing the stability of single-chain proteins by linker length and composition mutagenesis. Proc Natl Acad Sci USA 1998;95: 5929-34.
27. George RA, Heringa J. An analysis of protein domain linkers: Their classification and role in protein folding. Protein Eng 2002;15 871-9.
28. Katoh K, Kuma K, Miyata T, et al. Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inform 2005; 16:22-33.
29. Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-7.
30. Errami M, Geourjon C, Deleage G. Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures. Bioinformatics 2003;19:506-12.
31. Zhou H, Zhou Y. SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 2005;21:3615-21.
32. McGuffin LJ, Jones DT. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2003;19:874-81.
33. Portugaly E, Linial N, Linial M. EVEREST: A collection of evolutionary conserved protein domains. Nucleic Acids Res 2007;35:D241-6.
34. Gough J, Karplus K, Hughey R, et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001;313:903-19.