Linking Sequence and Structure
with Function

California Institute for Quantitative Biosciences (QB3)
University of California San Francisco
1700 4th Street, 5th Floor
San Francisco, CA 94158
USA

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

Pythoscape: Pythoscape is an extensible framework implemented in Python to generate and analyze protein similarity networks. To solve the issue of the complexity of data that can be associated with networks, Pythoscape was designed for rapid modification. The core Pythoscape package has an extensive set of functional plugins and tutorials, so that no development is needed for a less sophisticated user to create networks. For the more advanced user, Pythoscape provides API documentation for development of plugins that can utilize novel sources of meta-data.

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; 25(12):573-581.

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; 5(10):e10000541.

Supplementary data from
Atkinson HJ, Babbitt PC. Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry 2009; 48(46):11108-11116.

Supplementary data from
Mashiyama ST, McKerrow JH, Babbitt PC. T. brucei and human degradomes: a global comparison of sequences and structures; 2010; 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



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