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- person_outline Nicholas Furnham
Publications for FunTree
To what extent do structural changes in catalytic metal sites affect enzyme function?
[…] 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 […]
Reaction Decoder Tool (RDT): extracting features from chemical reactions
[…] 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 […]
The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection
[…] 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 […]
The evolution of enzyme function in the isomerases
[…] 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, […]
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
[…] 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 […]
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
[…] 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 […]
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