Linking Sequence and Structure
       with Function

The California Institute for Quantitative Biomedical Research (QB3)
1700 4th Street, 5th Floor
San Francisco, CA 94134

Alan Barber

Alan E. Barber II

Research Summary

My pricipal focus of study is of the evolution of life and more specifically the evolution of enzymes. I am fascinated by the process by which numerous catalytic mechanisms that can evolve from a single starting point and the manner by which evolution tuned and selected the enzymatic forms that carry out those chemistries.

To study enzyme evolution, we use protein similarity networks, which allows us to use graph theory to more efficiently study enzyme evolution. Using this technique in conjuction with phylogenetic trees, we are able to study the evolution of entire ancient enzyme superfamilies. The enzyme superfamilies that I have concentrated on for my thesis are that of the alkaline phosphatase superfamily and the co-evolution between cystein proteases like caspases and kinases. I have also developed a novel research tool called Pythoscape to faciliate this research.


Ph.D. 2012 (expected), University of California, San Francisco
B.S. 2006, College of Idaho (formerly Alberston College of Idaho), Gipson Honor Degree, Concentrations: Chemistry, Biology, Physics


The evolution of function in strictosidine synthase-like proteins.
Hicks MA, Barber AE 2nd , Giddings LA, Caldwell J, O'Connor SE, Babbitt PC. The evolution of function in strictosidine synthase-like proteins. Proteins: Struct., Funct., and Bioinf. 2011 Nov; 79(11):3082-98.
Charge asymmetries in hydration of polar solutes.
Mobley DL, Barber AE 2nd , Fennell CJ, Dill KA. Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14.


Pythoscape: A framework for creating and managing protein similarity networks
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.

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