College of Liberal Arts & Sciences

Modeling Interactomes

Oct 9, Tue 2007
2:00 pm, MRB 200

Dr. Ram Samudrala

University of Washington


A fundamental biological challenge is to understand how the linear information in an organism's genome is processed to produce the resulting behavior or phenotype. Genes are transcribed and translated into proteins that adopt three-dimensional conformations. Evolutionary processes ensure that a folded protein conformation interacts with its environment in a manner that is beneficial to the organism, using the protein to catalyze reactions, recognize cellular signals, build cellular structures, and to perform a host of other diverse biological functions.

Our research aims to understand these processes by developing computational algorithms to model, annotate, and understand the relationships between the sequences, structures, functions, and interactions of proteins, DNA, proteins and metabolites, at both the molecular and the genomic/systems levels.  The goal is to develop a coherent picture of the mechanistic basis (wiring diagram) of molecular and organismal structure, function, networks, and evolution within a fundamental scientific framework. We have applied our methods to more than fifty genomes/proteomes, encapsulated by the object-oriented Bioverse database and web application (  The individual structure and function prediction algorithms themselves are available at the Protinfo web server ( The talk will detail our current progress and provide an overview of the methodologies being pursued by our group to achieve the above goals, as well as recent discoveries and applications made using this framework.

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