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From Protein Sequence to Structure and Back...

Student-Run Applied & Math Seminar

Speaker: Patrice Koehl, UC Davis Computer Science and Genome Center
Location: 2112 MSB
Start time: Wed, Jan 20 2010, 12:10PM

The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In my presentation, I will explore the connection between the biological activities of proteins and geometry. I will cover three topics: (1) I will show that the geometry of a protein defines the size of its sequence space, (2) I will explore the possibility to encode the 3D structure of a protein as a linear structural sequence with minimal loss of information, and (3) I will describe a geometric representation of protein sequences that can be used to identify structural domains.