enzymefunction.org

 

 

This EFI workshop featured presentations describing the development and application of high throughput computational “tools” to facilitate functional assignment of unknown enzymes discovered in genome sequencing projects.  The glutathione transferase superfamily was used to demonstrate:

 

1) The use of sequence similarity networks (SSNs) to visualize relationships among members of functionally diverse enzyme superfamilies, identify unknowns, and aid the identification of their functions.


2)  The use of Cytoscape to visualize SSNs that are available in the Structure Function Linkage Database (SFLD).


3)  The use of homology modeling and docking tools to predict substrate specificities.

 

 

 

 

 

 

 

Cytscpape Video Tutorial - Brown 

SFLD Video Tutorial - Brown

SFLD PDF Tutorial - Brown

 

 

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. 

Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. (2009) PloS One 4, e4345.

 

Inference of functional properties from large-scale analysis of enzyme superfamilies.

Brown SD, Babbitt PC. (2011) J Biol Chem 287, 35-42.

 

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.

Lukk et al. (2012) Proc Natl Acad Sci USA 109, 4122-7.