Gabriel del Río Guerra

Instituto de Fisiologia Celular, UNAM. Circuito exterior s/n, 04510 Ciudad Universitaria, México, D.F.
gdelrio@ifc.unam.mx, gdelrio@buckinstitute.org

In the common scientific approach to study the mechanisms of action of biological organisms, these are fractioned in their components and the interactions among these components are determined. For instance, for the last 60 years proteins have been studied in terms of their components (i.e., amino acids) and the structural relationships between these: contact maps of amino acids in the three-dimensional structure of proteins. More recently, in the post-genomic era, the genetic components (i.e., genes) and the physical interactions between gene products (i.e., proteins) are being mapped to study biochemical mechanisms (e.g., metabolism, signal transduction). Hence, biological data is basically composed of the identity of components and interactions between components.

Thanks to the development of public databases, nowadays there is a large number of biological data available to researchers. As a consequence, computer applications such as database engines to store and retrieve this data, and computer clusters to process and mine biological data are now in demand.

We have used graph theory to represent biological data, in an attempt to mine the nature of biological mechanisms. Our studies are aimed at establishing the structure/function relationship of both protein function and biochemical mechanisms. Since the structure/function relationship of proteins has been studied thoroughly, these are being used as a model system to understand the nature of biochemical mechanisms. In order to achieve this, we implemented computer programs that incorporate the use of both a database engine and a computer cluster. Our studies revealed that proteins and biochemical mechanisms share topological properties that make them sensitive at their central components. A topological model is introduced to explain these similarities.