FunTree statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

FunTree specifications

Information


Unique identifier OMICS_10718
Name FunTree
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Nicholas Furnham

Publications for FunTree

FunTree citations

 (6)
library_books

To what extent do structural changes in catalytic metal sites affect enzyme function?

2018
PMCID: 5760197
PMID: 29161638
DOI: 10.1016/j.jinorgbio.2017.11.002

[…] te with each EC number we map the positions of the protein residues which coordinate the catalytic metal ion (metal-binding ligands, hereafter) onto the multiple sequence alignments obtained from the FunTree database . When the representative sequences presented in the FunTree alignment of a given superfamily did not include a metalloenzyme of interest, we added the sequence of the Metal-MACiE ent […]

library_books

Reaction Decoder Tool (RDT): extracting features from chemical reactions

2016
Bioinformatics
PMCID: 4920114
PMID: 27153692
DOI: 10.1093/bioinformatics/btw096

[…] Tools like EC-Blast (), FunTree (), MACiE () etc. use RDT in the background to mine and extract chemical information from thousands of enzyme reactions. The success rate of mapping is >99% when compared with manual AAM mappi […]

library_books

The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

2015
Nucleic Acids Res
PMCID: 4702933
PMID: 26740669
DOI: 10.1093/nar/gkv1356

[…] DB entries (–). Two databases use CATH structural domain classifications to shed light on protein function, Gene3D by assigning domain annotations and associated function predictions to proteomes and FunTree by attempting to better understand the evolution of protein function in superfamiles. Finally, the biological and medicinal interest in kinases fully justifies the effort spent in updating KLI […]

library_books

The evolution of enzyme function in the isomerases

2014
Curr Opin Struct Biol
PMCID: 4139412
PMID: 25000289
DOI: 10.1016/j.sbi.2014.06.002

[…] ully to map biological information to large sets of proteins []. However, it is also necessary to include associated changes of catalytic function during evolution preferably in an automated fashion. FunTree is a resource developed to accomplish that goal [] and it is maintained in collaboration with the CATH classification of protein structures []. By combining sequence, structure, phylogenetic, […]

library_books

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

2012
Nucleic Acids Res
PMCID: 3531114
PMID: 23203873
DOI: 10.1093/nar/gks1211

[…] stitute (EBI) (section f) that display information on the different multi-domain contexts in which this domain superfamily is observed [archschema section (f), ]. Section (g), provides a link to the FunTree () resource displaying phylogenetic information for enzyme superfamilies in CATH. FunTree is the product of a collaboration between the Thornton and Orengo groups and was developed and is mana […]

library_books

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

2012
PLoS Comput Biol
PMCID: 3291543
PMID: 22396634
DOI: 10.1371/journal.pcbi.1002403

[…] enzyme mechanisms designed to provide a wide range of E.C. defined functions, to identify 276 enzymatic CATH superfamilies with adequate structural and functional data suitable for processing by the FunTree pipeline. The superfamilies included representatives from 189 different fold groups and all four CATH classes.For each superfamily and their SSG/MDA clusters, we generated a number of visualis […]

Citations

Looking to check out a full list of citations?

FunTree institution(s)
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, UK
FunTree funding source(s)
Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K020013/1]; MRC Research Methodology Fellowship [MRC: MR/K020420]

FunTree reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FunTree