Databases
The Structure Function Linkage Database: A tool for the investigation of protein sequence, structure, and function. In particular, it aims to provide explicit information concerning how a given protein, or family of proteins, delivers chemical functionality.
Software
Intersect: A program for biological sequence analysis. More precisely, it is post-processing program for sets of output files generated by sequence database searches. Intersect identifies sequences reported across sets of output files and displays this information visually.
Shotgun: We have developed and used the Shotgun program to identify both new superfamily members and to reconstruct several known enzyme superfamilies using BLAST database searches. An analysis of the false-positive rates generated in the analysis and other control experiments provides evidence that high Shotgun scores indicate real evolutionary relationships. Shotgun is also a useful tool for identifying subgroup relationships within superfamilies and for testing hypotheses about related protein families.
Datasets and Documents
Supplementary data
from
Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using
sequence similarity networks for visualization of relationships across diverse
protein superfamilies.
PLoS One
2009; 4(2): e4345.
Supplementary data
from
Atkinson HJ, Babbitt PC, Sajid M. The global cysteine peptidase landscape in
parasites. Trends Parasitol
2009; submitted.
Supplementary data
from
Atkinson HJ, Babbitt PC. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol
2009; submitted.
Supplementary data
from
Atkinson HJ, Babbitt PC. Glutathione transferases are structural and functional outliers in the thioredoxin fold.
2009; in preparation.
Talks
Pitfalls (& Solutions) for Assigning molecular Function from Structural Similarities: Mechanistically Diverse Enzyme Superfamilies A talk from the Automated Function Prediction Special Interest Group on June 24th 2005, Detroit, MI, given by Prof. Patricia Babbitt
Classification of Mechanistically Diverse Enzyme Superfamilies According to Similarities in Reaction Mechanism A talk from the Structural Bioinformatics and Computational Biophysics ISMB satellite meeting on July 18th 2008, Toronto, Canada, given by Dr Daniel Almonacid
