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Exploring Protein Sequence Space

Student-Run Applied & Math Seminar

Speaker: Paul Mach, UC Davis
Location: 2112 MSB
Start time: Wed, May 28 2008, 12:10PM

Chains of amino acids fold into complex three-dimensional shapes. To better understand this process, the set of sequences that are able to fold into a given protein structure are analyzed. This subset of all possible sequences can help identify which amino acid types, in what locations, are important to a specific shape. The described procedure samples from this set using a heuristic Monte Carlo search. Energies calculated at each step, using a full atom model, are used for direction. To speed the calculation, an analytical method to compute the solvation energy of a molecule is introduced. This method is based on the Voronoi Complex of the union of spheres that represent the atoms of the protein. This, along with numerous implementation improvements, make the problem computationally tractable.