FunTree: A resource for exploring the functional evolution of structurally defined enzyme superfamilies

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Furnham, Nicholas ^a   Sillitoe, Ian ^b   Holliday, Gemma L ^a   Cuff, Alison L ^b   Rahman, Syed A ^a   Laskowski, Roman A ^a   Orengo, Christine A ^b   Thornton, Janet M ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL REACTION; COMPUTER PROGRAM; DATA PROCESSING; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; EVOLUTION; FACTUAL DATABASE; FUNTREE; METABOLITE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ALIGNMENT;

BIOLOGICAL EVOLUTION; DATABASES, PROTEIN; ENZYMES; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 84861139534     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr852     Document Type: Article

References (32)

1. Rentzsch,R. and Orengo,C.A. (2009) Protein function prediction-the power of multiplicity. Trends Biotechnol., 27, 210-219.
2. Bartlett,G.J., Borkakoti,N. and Thornton,J.M. (2003) Catalysing new reactions during evolution: economy of residues and mechanism. J. Mol. Biol., 331, 829-860. (Pubitemid 36957867)
3. Brown,S.D., Gerlt,J.A., Seffernick,J.L. and Babbitt,P.C. (2006) A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol., 7, R8.
4. Glasner,M.E., Gerlt,J.A. and Babbitt,P.C. (2006) Evolution of enzyme superfamilies. Curr. Opin. Chem. Biol., 10, 492-497. (Pubitemid 44375064)
5. Todd,A.E., Orengo,C.A. and Thornton,J.M. (1999) Evolution of protein function, from a structural perspective. Curr. Opin. Chem. Biol., 3, 548-556. (Pubitemid 29447489)
6. Cuff,A.L., Sillitoe,I., Lewis,T., Clegg,A.B., Rentzsch,R., Furnham,N., Pellegrini-Calace,M., Jones,D., Thornton,J. and Orengo,C.A. Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res., 39, D420-D426.
7. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
8. Lees,J., Yeats,C., Redfern,O., Clegg,A. and Orengo,C. Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res., 38, D296-D300.
9. Holliday,G.L., Almonacid,D.E., Bartlett,G.J., O'Boyle,N.M., Torrance,J.W., Murray-Rust,P., Mitchell,J.B. and Thornton,J.M. (2007) MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res., 35, D515-D520. (Pubitemid 46056262)
10. Porter,C.T., Bartlett,G.J. and Thornton,J.M. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res., 32, D129-D133. (Pubitemid 38081621)
11. Furnham,N., Garavelli,J.S., Apweiler,R. and Thornton,J.M. (2009) Missing in action: enzyme functional annotations in biological databases. Nat. Chem. Biol., 5, 521-525.
12. Schnoes,A.M., Brown,S.D., Dodevski,I. and Babbitt,P.C. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605.
13. Orengo,C.A. (1999) CORA-topological fingerprints for protein structural families. Protein Sci., 8, 699-715.
14. McLachlan,A. (1982) Rapid comparison of protein structures. Acta Crystallog. Sect. A, 38, 871-873.
15. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
16. Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257. (Pubitemid 32619966)
17. Bashton,M. and Chothia,C. (2007) The generation of new protein functions by the combination of domains. Structure, 15, 85-99. (Pubitemid 46091745)
18. Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
19. Tamuri,A.U. and Laskowski,R.A. (2010) ArchSchema: a tool for interactive graphing of related Pfam domain architectures. Bioinformatics, 26, 1260-1261.
20. Katoh,K. and Toh,H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform., 9, 286-298. (Pubitemid 351890825)
21. Ruan,J., Li,H., Chen,Z., Coghlan,A., Coin,L.J., Guo,Y., Heriche,J.K., Hu,Y., Kristiansen,K., Li,R. et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36, D735-D740. (Pubitemid 351149816)
22. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2009) GenBank. Nucleic Acids Res., 37, D26-D31.
23. IUBMB. (1992) IUBMB (1992) Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes.
24. Kanehisa,M. and Goto,S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30. (Pubitemid 30047706)
25. Rahman,S., Bashton,M., Holliday,G., Schrader,R. and Thornton,J. (2009) Small Molecule Subgraph Detector (SMSD) toolkit. J. Cheminformat., 1, 12.
26. Suzuki,R. and Shimodaira,H. (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22, 1540-1542. (Pubitemid 43985330)
27. Valdar,W.S. (2002) Scoring residue conservation. Proteins, 48, 227-241.
28. Orengo,C.A., Taylor,W.R. and Russell,F.D. (1996) Methods in Enzymology, Vol. 266. Academic Press, San Diego, USA, pp. 617-635.
29. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ (5 October 2011, date last accessed).
30. Waterhouse,A.M., Procter,J.B., Martin,D.M., Clamp,M. and Barton,G.J. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
31. Laskowski,R.A. (2009) PDBsum new things. Nucleic Acids Res., 37, D355-D359.
32. Cock,P.J., Antao,T., Chang,J.T., Chapman,B.A., Cox,C.J., Dalke,A., Friedberg,I., Hamelryck,T., Kauff,F., Wilczynski,B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.